Water is required for proton transfer from aspartate-96 to the bacteriorhodopsin Schiff base

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.

Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A

Proton transfer in biological systems is thought to often proceed through hydrogen-bonded chains of water molecules. The ion channel, gramicidin A (gA), houses within its helical structure just such a chain. Using the density functional theory based ab initio molecular dynamics Car-Parrinello method, the structure and dynamics of proton diffusion through a polyglycine analog of the gA ion channel has been investigated. In the channel, a proton, which is initially present as hydronium (H3O+), rapidly forms a strong hydrogen bond with a nearest neighbor water, yielding a transient H5O2+ complex. As in bulk water, strong hydrogen bonding of this complex to a second neighbor solvation shell is required for proton transfer to occur. Within gA, this second neighbor shell included not only a channel water molecule but also a carbonyl of the channel backbone. The present calculations suggest a transport mechanism in which a priori carbonyl solvation is a requirement for proton transfer.

Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study

The proton transfer activity of the light-driven proton pump, bacteriorhodopsin (bR) in the photochemical cycle might imply internal water molecules. The free energy of inserting water molecules in specific sites along the bR transmembrane channel has been calculated using molecular dynamics simulations based on a microscopic model. The existence of internal hydration is related to the free energy change on transfer of a water molecule from bulk solvent into a specific binding site. Thermodynamic integration and perturbation methods were used to calculate free energies of hydration for each hydrated model from molecular dynamics simulations of the creation of water molecules into specific protein-binding sites. A rigorous statistical mechanical formulation allowing the calculation of the free energy of transfer of water molecules from the bulk to a protein cavity is used to estimate the probabilities of occupancy in the putative bR proton channel. The channel contains a region lined primarily by nonpolar side-chains. Nevertheless, the results indicate that the transfer of four water molecules from bulk water to this apparently hydrophobic region is thermodynamically permitted. The column forms a continuous hydrogen-bonded chain over 12 A between a proton donor, Asp 96, and the retinal Schiff base acceptor. The presence of two water molecules in direct hydrogen-bonding association with the Schiff base is found to be strongly favorable thermodynamically. The implications of these results for the mechanism of proton transfer in bR are discussed.

Structure and dynamics of a proton wire: a theoretical study of H+ translocation along the single-file water chain in the gramicidin A channel

The rapid translocation of H+ along a chain of hydrogen-bonded water molecules, or proton wire, is thought to be an important mechanism for proton permeation through transmembrane channels. Computer simulations are used to study the properties of the proton wire formed by the single-file waters in the gramicidin A channel. The model includes the polypeptidic dimer, with 22 water molecules and one excess proton. The dissociation of the water molecules is taken into account by the "polarization model" of Stillinger and co-workers. The importance of quantum effects due to the light mass of the hydrogen nuclei is examined with the use of discretized Feynman path integral molecular dynamics simulations. Results show that the presence of an excess proton in the pore orients the single-file water molecules and affects the geometry of water-water hydrogen bonding interactions. Rather than a well-defined hydronium ion OH3+ in the single-file region, the protonated species is characterized by a strong hydrogen bond resembling that of O2H5+. The quantum dispersion of protons has a small but significant effect on the equilibrium structure of the hydrogen-bonded water chain. During classical trajectories, proton transfer between consecutive water molecules is a very fast spontaneous process that takes place in the subpicosecond time scale. The translocation along extended regions of the chain takes place neither via a totally concerted mechanism in which the donor-acceptor pattern would flip over the entire chain in a single step, nor via a succession of incoherent hops between well-defined intermediates. Rather, proton transfer in the wire is a semicollective process that results from the subtle interplay of rapid hydrogen-bond length fluctuations along the water chain. These rapid structural fluctuations of the protonated single file of waters around an average position and the slow movements of the average position of the excess proton along the channel axis occur on two very different time scales. Ultimately, it is the slow reorganization of hydrogen bonds between single-file water molecules and channel backbone carbonyl groups that, by affecting the connectivity and the dynamics of the single-file water chain, also limits the translocation of the proton across the pore.

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.

The heme redox center of chloroplast cytochrome f is linked to a buried five-water chain

The crystal structure of the 252-residue lumen-side domain of reduced cytochrome f, a subunit of the proton-pumping integral cytochrome b6f complex of oxygenic photosynthetic membranes, was determined to a resolution of 1.96 A from crystals cooled to -35 degrees. The model was refined to an R-factor of 15.8% with a 0.013-A RMS deviation of bond lengths from ideality. Compared to the structure of cytochrome f at 20 degrees, the structure at -35 degrees has a small change in relative orientation of the two folding domains and significantly lower isotropic temperature factors for protein atoms. The structure revealed an L-shaped array of five buried water molecules that extend in two directions from the N delta 1 of the heme ligand His 25. The longer branch extends 11 A within the large domain, toward Lys 66 in the prominent basic patch at the top of the large domain, which has been implicated in the interaction with the electron acceptor, plastocyanin. The water sites are highly occupied, and their temperature factors are comparable to those of protein atoms. Virtually all residues that form hydrogen bonds with the water chain are invariant among 13 known cytochrome f sequences. The water chain has many features that optimize it as a proton wire, including insulation from the protein medium. It is suggested that this chain may function as the lumen-side exit port for proton translocation by the cytochrome b6f complex.

Structure and dynamics of hydronium in the ion channel gramicidin A

The effects of the hydronium ion, H(3)0+, on the structure of the ion channel gramicidin A and the hydrogen-bonded network of waters within the channel were studied to help elucidate a possible mechanism for proton transport through the channel. Several classical molecular dynamics studies were carried out with the hydronium in either the center of a gramicidin monomer or in the dimer junction. Structural reorganization of the channel backbone was observed for different hydronium positions, which were most apparent when the hydronium was within the monomer. In both cases the average O-O distance between the hydronium ion and its nearest neighbor water molecule was found to be approximately 2.55 A, indicating a rather strong hydrogen bond. Importantly, a subsequent break in the hydrogen-bonded network between the nearest neighbor and the next-nearest neighbor(approximately 2.7 -3.0 A) was repeatedly observed. Moreover, the carbonyl groups of gramicidin A were found to interact with the charge on the hydronium ion, helping in its stabilization. These facts may have significant implications for the proton hopping mechanism. The presence of the hydronium ion in the channel also inhibits to some degree the reorientational motions of the channel water molecules.

Determination of the transiently lowered pKa of the retinal Schiff base during the photocycle of bacteriorhodopsin

Reprotonation of the transiently deprotonated retinal Schiff base in the bacteriorhodopsin photocycle is greatly slowed when the proton donor Asp-96 is removed with site-specific mutagenesis, but its rate is restored upon adding azide or other weak acids such as formate and cyanate. As expected, between pH 3 and 7 the rate of Schiff base protonation in the photocycle of the D96N mutant correlates with the concentrations of the acid forms of these agents. Dissection of the rates in the biexponential reprotonation kinetics of the Schiff base between pH 7 and 9 yielded calculated rate constants for the protonation equilibrium. Their dependencies on pH and azide or cyanate concentrations are consistent with both earlier suggested mechanisms: (i) azide and other weak acids may function as proton carriers in the protonation equilibrium of the Schiff base, or (ii) the binding of their anionic forms may catalyze proton conduction to and from the Schiff base. The measured rate constants allow the calculation of the pKa of the Schiff base during its reprotonation in the photocycle of D96N. It is 8.2-8.3, a value much below the pKa determined earlier in unphotolyzed bacteriorhodopsin.

Structure of the N intermediate of bacteriorhodopsin revealed by x-ray diffraction

X-ray diffraction experiments revealed the structure of the N photointermediate of bacteriorhodopsin. Since the retinal Schiff base is reprotonated from Asp-96 during the M to N transition in the photocycle, and Asp-96 is reprotonated during the lifetime of the N intermediate, or immediately after, N is a key intermediate for understanding the light-driven proton pump. The N intermediate accumulates in large amounts during continuous illumination of the F171C mutant at pH 7 and 5 degrees Celsius. Small but significant changes of the structure were detected in the x-ray diffraction profile under these conditions. The changes were reversible and reproducible. The difference Fourier map indicates that the major change occurs near helix F. The observed diffraction changes between N and the original state were essentially identical to the diffraction changes reported for the M intermediate of the D96N mutant of bacteriorhodopsin. Thus, we find that the protein conformations of the M and N intermediates of the photocycle are essentially the same, in spite of the fact that in M the Schiff base is unprotonated and in N it is protonated. The observed structural change near helix F will increase access of the Schiff base and Asp-96 to the cytoplasmic surface and facilitate the proton transfer events that begin with the decay of the M state.

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

The effects of excitation light intensity on the kinetics of the bacteriorhodopsin photocycle were investigated. The earlier reported intensity-dependent changes at 410 and 570 nm are explained by parallel increases in two of the rate constants, for proton transfers to D96 from the Schiff base and from the cytoplasmic surface, without changes in the others, as the photoexcited fraction is increased. Thus, it appears that the pKa of D96 is raised by a cooperative effect within the purple membrane. This interpretation of the wild-type kinetics was confirmed by results with several mutant proteins, where the rates are well separated in time and a model-dependent analysis is unnecessary. Based on earlier results that demonstrated a structural change of the protein after deprotonation of the Schiff base that increases the area of the cytoplasmic surface, and the effects of high hydrostatic pressure and lowered water activity on the photocycle steps in question, we suggest that the pKa of D96 is raised by a lateral pressure that develops when other bacteriorhodopsin molecules are photoexcited within the two-dimensional lattice of the purple membrane. Expulsion of no more than a few water molecules bound near D96 by this pressure would account for the calculated increase of 0.6 units in the pKa.

Retention of bacteriorhodopsin activity in dried sol-gel glass

The D96N mutant form of bacteriorhodopsin (bR) purple membrane fragments isolated from Halobacterium salinarium has been entrapped in sol-gel glass and dried. The photo-activity of the bR was monitored during drying over a period of 60 days. The entrapped bR was initially dried at 4 degrees C followed by room temperature storage. Samples showing constant activity after storage at 4 degrees C lost further activity at room temperature, eventually reaching a level where the activity remained constant. Upon further drying at 100 degrees in a vacuum oven the glass lost an additional 11.4 +/- 1.3% weight and all remaining activity.

Cooperative phenomena in the photocycle of D96N mutant bacteriorhodopsin

The M intermediate decay in the photocycle of D96N mutant bacteriorhodopsin does not depend on the light intensity of the exciting flash. Cooperative phenomena in the photocycle are revealed after addition of azide causing acceleration of the M decay and making it kinetically well separated from the N decay. Increase in the light intensity induces slight deceleration of the M decay and significant acceleration of the N decay. The data obtained directly confirm our recent model [Komrakov and Kaulen (1995) Biophys. Chem. 56, 113-119], according to which appearance of the Mslow intermediate in the photocycle of the wild type bR at high light intensity is due to destabilization of the N intermediate leading to the acceleration of the N-->M and N-->bR reactions.

Molecular dynamics study of the M412 intermediate of bacteriorhodopsin

Molecular dynamics simulations have been carried out to study the M412 intermediate of bacteriorhodopsin's (bR) photocycle. The simulations start from two simulated structures for the L550 intermediate of the photocycle, one involving a 13-cis retinal with strong torsions, the other a 13,14-dicis retinal, from which the M412 intermediate is initiated through proton transfer to Asp-85. The simulations are based on a refined structure of bR568 obtained through all-atom molecular dynamics simulations and placement of 16 waters inside the protein. The structures of the L550 intermediates were obtained through simulated photoisomerization and subsequent molecular dynamics, and simulated annealing. Our simulations reveal that the M412 intermediate actually comprises a series of conformations involving 1) a motion of retinal; 2) protein conformational changes; and 3) diffusion and reconfiguration of water in the space between the retinal Schiff base nitrogen and the Asp-96 side group. (1) turns the retinal Schiff base nitrogen from an early orientation toward Asp-85 to a late orientation toward Asp-96; (2) disconnects the hydrogen bond network between retinal and Asp-85 and tilts the helix F of bR, enlarging bR's cytoplasmic channel; (3) adds two water molecules to the three water molecules existing in the cytoplasmic channel at the bR568 stage and forms a proton conduction pathway. The conformational change (2) of the protein involves a 60 degrees bent of the cytoplasmic side of helix F and is induced through a break of a hydrogen bond between Tyr-185 and a water-side group complex in the counterion region.

Functional significance of a protein conformation change at the cytoplasmic end of helix F during the bacteriorhodopsin photocycle

The second half of the photocycle of the light-driven proton pump bacteriorhodopsin includes proton transfers between D96 and the retinal Schiff base (the M to N reaction) and between the cytoplasmic surface and D96 (decay of the N intermediate). The inhibitory effects of decreased water activity and increased hydrostatic pressure have suggested that a conformational change resulting in greater hydration of the cytoplasmic region is required for proton transfer from D96 to the Schiff base, and have raised the possibility that the reversal of this process might be required for the subsequent reprotonation of D96 from the cytoplasmic surface. Tilt of the cytoplasmic end of helix F has been suggested by electron diffraction of the M intermediate. Introduction of bulky groups, such as various maleimide labels, to engineered cysteines at the cytoplasmic ends of helices A, B, C, E, and G produce only minor perturbation of the decays of M and N, but major changes in these reactions when the label is linked to helix F. In these samples the reprotonation of the Schiff base is accelerated and the reprotonation of D96 is strongly retarded. Cross-linking with benzophenone introduced at this location, but not at the others, causes the opposite change: the reprotonation of the Schiff base is greatly slowed while the reprotonation of D96 is accelerated. We conclude that, consistent with the structure from diffraction, the proton transfers in the second half of the photocycle are facilitated by motion of the cytoplasmic end of helix F, first away from the center of the protein and then back.

The Ca2+ binding to deionized monomerized and to retinal removed bacteriorhodopsin

In our continuing effort to characterize the metal cation binding in bacteriorhodopsin (bR) using Ca(2+)-specific electrodes, potentiometric titration was carried out on deionized solubilized bR (containing monomeric units) and deionized bacterioopsin (bR with its retinal removed). Scatchard plots were analyzed. The monomer was found to have plots similar to those of the trimer, suggesting that the binding sites in bR are localized within the protein monomer unit and not between the molecules within the trimer structure. This also supports the previous assumption that the curvature in the Scatchard plot of regenerated bR is not due to cooperativity of metal cation within the trimer, but rather due to multiple sites. Recent studies further support the finding that the curved Scatchard plot is not due to the cooperativity between the metal ions in the two high affinity sites, wherever they are. The results of the analysis of the Scatchard plot for deionized bacterioopsin have shown a change in the binding characteristics of the high affinity but not the low affinity sites from that observed in bR. This result supports previous conclusions that metal cations in the high affinity sites are not far from the retinal cavity.

High-pressure near-infrared Raman spectroscopy of bacteriorhodopsin light to dark adaptation

Near-infrared (NIR) Raman spectroscopy is employed as an in situ probe of the chromophore conformation to study the light to dark-adaptation process in bacteriorhodopsin (bR) at variable pressure and temperature in the absence of undesired photoreactions. In dark-adapted bR deconvolution of the ethylenic mode into bands assigned to the all-trans (1526 cm-1) and 13-cis (1534 cm-1) isomers yields a 13-cis to all-trans ratio equal to 1 at ambient pressure (Schulte et al., 1995, Appl. Spectrosc. 49:80-83). Detailed spectroscopic evidence is presented that at high pressure the equilibrium is shifted toward the 13-cis isomers and that the light to dark adaptation kinetics is accelerated. The change in isomeric composition with temperature and pressure as well as the kinetics support a two-state model activation volumes of -16 ml/mol for the transition of 13-cis to all-trans and -22 ml/mol for the reverse process. These compare with a conformational volume difference of 6.6 ml/mol, which may be attributed to the ionization of one or two residues or the formation of three hydrogen bonds.

Effects of hydrostatic pressure on the kinetics reveal a volume increase during the bacteriorhodopsin photocycle

A protein structural change in the photocycle of the proton pump, bacteriorhodopsin, detected earlier in the M photointermediate by diffraction, consists mainly of changes at the cytoplasmic surface that include an outward tilt of the cytoplasmic end of helix F. Such a conformational rearrangement would result in greater exposure of the interhelical cavity to the medium, increased binding of water, and thus an increase in volume. In order to correlate the structural change with the kinetics of the photoreaction cycle, we measured the effects of hydrostatic pressure between 1 bar and 1 kbar on the rate constants of the photocycles of wild type bacteriorhodopsin and the D96N mutant. Combining the results provided all of the activation volumes and, therefore, the changes of volume in the various states after the K photointermediate is formed. There is an approximately 32 mL/mol volume increase after deprotonation of the retinal Schiff base to the extracellular side, during the M1 --> M2 reaction, that is not reversed until well after its reprotonation from the cytoplasmic side. The magnitude of this volume increase is about as predicted by the increase of the lattice constant in the M state. It occurs in the photocycle at the proposed reprotonation switch, supporting the idea that this conformation change is what alters the accessibility of the Schiff base from one membrane side to the other. Additionally, we observe a large positive (approximately 50 mL/mol) activation volume for proton exchange between D96 and the Schiff base of the wild type protein.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteriorhodopsin: a paradigm for proton pumps?

Recent studies of the photochemistry of wild type and mutant bacteriorhodopsins, their proton release and uptake kinetics, and their X-ray diffraction structure have suggested a hypothesis for the way energy is coupled in this light-driven proton pump. The first and critical step in converting light energy to a vectorial proton potential is the transfer of the Schiff base proton to D85 which causes dissociation of the Schiff base-counterion complex. Removal of this primarily coulombic interaction destabilizes the protein structure, and results in transition to an alternative conformation in which the two proton conduction pathways between the active site and the membrane surfaces are reorganized. Recovery of the initial charge state of the Schiff base and D85 must therefore occur through a series of unidirectional proton transfers that create a transmembrane electrochemical proton gradient. Passage of the transported proton through the two peripheral protein domains appears to utilize hydrogen bonded networks containing aspartate, arginine and bound water. This kind of mutual interaction between the active site and the protein conformation that determines the conductive pathways to the two membrane surfaces may have relevance to ion pumps in general.

Relationship of proton release at the extracellular surface to deprotonation of the schiff base in the bacteriorhodopsin photocycle

The surface potential of purple membranes and the release of protons during the bacteriorhodopsin photocycle have been studied with the covalently linked pH indicator dye, fluorescein. The titration of acidic lipids appears to cause the surface potential to be pH-dependent and causes other deviations from ideal behavior. If these anomalies are neglected, the appearance of protons can be followed by measuring the absorption change of fluorescein bound to various residues at the extracellular surface. Contrary to widely held assumption, the activation enthalpies of kinetic components, deuterium isotope effects in the time constants, and the consequences of the D85E, F208R, and D212N mutations demonstrate a lack of direct correlation between proton transfer from the buried retinal Schiff base to D85 and proton release at the surface. Depending on conditions and residue replacements, the proton release can occur at any time between the protonation of D85 and the recovery of the initial state. We conclude that once D85 is protonated the proton release at the extracellular protein surface is essentially independent of the chromophore reactions that follow. This finding is consistent with the recently suggested version of the alternating access mechanism of bacteriorhodopsin, in which the change of the accessibility of the Schiff base is to and away from D85 rather than to and away from the extracellular membrane surface.

Functional interactions in bacteriorhodopsin: a theoretical analysis of retinal hydrogen bonding with water

The light-driven proton pump, bacteriorhodopsin (bR) contains a retinal molecule with a Schiff base moiety that can participate in hydrogen-bonding interactions in an internal, water-containing channel. Here we combine quantum chemistry and molecular mechanics techniques to determine the geometries and energetics of retinal Schiff base-water interactions. Ab initio molecular orbital calculations are used to determine potential surfaces for water-Schiff base hydrogen-bonding and to characterize the energetics of rotation of the C-C single bond distal and adjacent to the Schiff base NH group. The ab initio results are combined with semiempirical quantum chemistry calculations to produce a data set used for the parameterization of a molecular mechanics energy function for retinal. Using the molecular mechanics force field the hydrated retinal and associated bR protein environment are energy-minimized and the resulting geometries examined. Two distinct sites are found in which water molecules can have hydrogen-bonding interactions with the Schiff base: one near the NH group of the Schiff base in a polar region directed towards the extracellular side, and the other near a retinal CH group in a relatively nonpolar region, directed towards the cytoplasmic side.

Energy coupling in an ion pump. The reprotonation switch of bacteriorhodopsin

The active site of an ion pump must communicate alternately with the two opposite membrane surfaces. In the light-driven proton pump, bacteriorhodopsin, the retinal Schiff base is first the proton donor to D85 (with access to the extracellular side), and then it becomes the acceptor of the proton of D96 (with access to the cytoplasmic side). This "reprotonation switch" has been associated with a protein conformation change observed during the photocycle. When D85 is replaced with asparagine, the pKa value of the Schiff base is lowered from above 13 to about 9. We determined the direction of the loss or gain of the Schiff base proton in unphotolyzed and in photoexcited D85N, and the D85N/D96N and D85N/D96A double mutants, in order to understand the intrinsic and the induced connectivities of the Schiff base to the two membrane surfaces. The influence of D96 mutations on proton exchange and on acceleration of proton shuttling to the surface by azide indicated that in either case the access of the Schiff base on D85N mutants is to the cytoplasmic side. In the wild-type protein (but with the pKa of the Schiff base lowered by 13-trifluoromethyl retinal substitution) the results suggested that the Schiff base can communicate also with the extracellular side. Raising the pH without illumination of D85N so as to deprotonate the Schiff base caused the same, or nearly the same, change of X-ray scattering as observed when the Schiff base deprotonates during the wild-type photocycle. The results link the charge state of the active site to the global protein conformation and to the connectivity of the Schiff base proton to the membrane surfaces. Their relationship suggests that the conformation of the unphotolyzed wild-type protein is stabilized by coulombic interaction of the Schiff base with its counter-ion. A proton is translocated across the membrane after light-induced transfer of the Schiff base proton to D85, because the protein assumes an alternative conformation that separates the donor from the acceptor and opens new conduction pathways between the active site and the two membrane surfaces.

Detection of a water molecule in the active-site of bacteriorhodopsin: hydrogen bonding changes during the primary photoreaction

FTIR-difference spectroscopy in combination with site-directed mutagenesis has been used to investigate the role of water during the photocycle of bacteriorhodopsin. At least one water molecule is detected which undergoes an increase in H-bonding during the primary bR-->K phototransition. Bands due to water appear in the OH stretch region of the bR-->K FTIR-difference spectrum which downshift by approximately 12 cm-1 when the sample is hydrated with H2(18)O. In contrast to 2H2O, the H2(18)O-induced shift is not complete, even after 24 h of hydration. This indicates that even though water is still able to exchange protons with the outside medium, it is partially trapped in the interior of the protein. In the mutant Y57D, these bands are absent while a new set of bands appear at much lower frequencies which undergo H2(18)O-induced shifts. It is concluded that the water molecule we detect is located inside the bR active-site and may interact with Tyr-57. The change in its hydrogen-bonding strength is most likely due to the photoinduced all-trans-->13-cis isomerization of the retinal chromophore and the associated movement of the positively charged Schiff base during the bR-->K transition. In contrast, a second water molecule, whose infrared difference bands are not affected by the Y57D mutation, appears to undergo a decrease in hydrogen bonding during the K-->L and L-->M transitions.

The retinal Schiff base-counterion complex of bacteriorhodopsin: changed geometry during the photocycle is a cause of proton transfer to aspartate 85

Bacteriorhodopsin contains all-trans-retinal linked via a protonated Schiff base to K216. The proton transport in this pump is initiated by all-trans to 13-cis photoisomerization of the retinal and the ensuing transfer of the Schiff base proton to D85. Changed geometrical relationship of the Schiff base and D85 after the photoisomerization is a possible reason for the proton transfer. We introduced small volume/shape changes with site-specific mutagenesis of residues V49 and A53 that contact the side chain of K216, in order to force the Schiff base into somewhat different positions relative to D85. Earlier [Zimányi, L., Váró, G., Chang, M., Ni, B., Needleman, R., & Lanyi, J. K. (1992) Biochemistry 31, 8535-8543] we had described the kinetics of absorbance changes in the microsecond to millisecond time range after photoexcitation with the scheme L<-->M1<-->M2 + H+ (where the first equilibrium is the internal proton transfer and the second is proton release on the extracellular surface). Testing it at various pH values with mutants, where selected rate constants are changed, now confirms the validity of this scheme. The kinetics of the M state thus allowed examination of the transient equilibrium that develops in the L<-->M1 reaction and represents the redistribution of the proton between the Schiff base and D85. From the structure of the protein, the V49A and V49M residue replacements were both predicted to cause decreased alignment of the Schiff base and D85, and indeed we found that they both changed the equilibrium toward the protonated Schiff base. In contrast, the residue replacements A53V and A53G were predicted to move the Schiff base in opposite directions, away from and closer to alignment with D85, respectively. The former indeed changed the equilibrium toward the protonated Schiff base and the latter toward the deprotonated Schiff base. In addition, the hydroxyl stretch band of a bound water in the L state was affected by all mutations that disfavor proton transfer to D85. We conclude that the geometry of the proton donor and acceptor in the Schiff base-D85 pair, mediated by bound water, is a determinant of the proton transfer equilibrium.

Two progressive substrates of the M-intermediate can be identified in glucose-embedded, wild-type bacteriorhodopsin

Glucose-embedded bacteriorhodopsin shows M-intermediates with different Amide I infrared bands when samples are illuminated at 240 or 260 K, in contrast with fully hydrated samples where a single M-intermediate is formed at all temperatures. In hydrated, but not in glucose-embedded specimens, the N intermediate is formed together with M at 260 K. Both Fourier transform infrared and electron diffraction data from glucose-embedded bacteriorhodopsin suggest that at 260 K a mixture is formed of the M-state that is trapped at 240 K, and a different M-intermediate (MN) that is also formed by mutant forms of bacteriorhodopsin that lack a carboxyl group at the 96 position, necessary for the M to N transition. The fact that an MN species is trapped in glucose-embedded, wild-type bacteriorhodopsin suggests that the glucose samples lack functionally important water molecules that are needed for the proton transfer aspartate 96 to the Schiff base (and, thus, to form the N-intermediate); thus, aspartate 96 is rendered ineffective as a proton donor.

The bacteriorhodopsin photocycle: direct structural study of two substrates of the M-intermediate

Changes in protein structure that occur during the formation of the M photointermediate of bacteriorhodopsin can be directly visualized by electron diffraction techniques. A modified preparation technique for glucose-embedded crystals was employed to ensure sufficient hydration of the crystals, which was needed for the formation of the M intermediate at low temperature. Samples containing a high percentage of the M intermediate were trapped by rapidly cooling the crystals with liquid nitrogen after illumination with filtered green light at 240 and 260 K, respectively. Difference Fourier projection maps are presented for the M intermediates formed at these two temperatures. The diffraction data clearly show that statistically significant structural changes occur upon formation of the M intermediate at 240 K and then further upon formation of the second specimen that is produced at 260 K.

Phylogenetic relationships among bacteriorhodopsins

Retinal-containing proteins of archaea comprise a single family of homologous proteins that fall into three clusters correlating with function: the proton-transporting bacteriorhodopsins, the chloride-transporting halorhodopsins and the colour-discriminating sensory rhodopsins. Statistical and phylogenetic analyses, a multiple alignment and average hydropathy and similarity plots of these protein sequences are presented. Available evidence suggests that sequence conservation generally correlates with functional significance. Little or no evidence substantiates the proposal that these proteins arose by a tandem intragenic duplication event. The bacterial rhodopsin family appears to have evolved from a common ancestor without recognizable intragenic rearrangements.

Interaction of aspartate-85 with a water molecule and the protonated Schiff base in the L intermediate of bacteriorhodopsin: a Fourier-transform infrared spectroscopic study

Fourier-transform infrared spectra were recorded at 170 K before and after irradiating the Asp85-->Asn mutant of bacteriorhodopsin. The difference spectrum exhibits protein bands such as those due to the perturbations of Asp96 and Asp115 and the N-H stretching vibration of tryptophan, characteristic of the L minus all-trans-bacteriorhodopsin spectrum of the wild-type protein. However, some vibrational bands of the peptide backbone and the chromophore are different from L and more characteristic of N of the wild-type protein. Remarkably, the shift observed for the vibrational band due to an internal water molecule upon L formation [Maeda, Sasaki, Shichida, and Yoshizawa (1992) Biochemistry 31, 462-467] is absent. These changes in the spectrum of the mutant could originate from the destruction of a hydrogen-bonding system consisting of Asp85, the water molecule, and the Schiff base, upon replacement of Asp85 with asparagine. These observations constitute direct evidence for the interaction of water with Asp85 at the time when it is protonated by the Schiff base.

Proton translocation mechanism and energetics in the light-driven pump bacteriorhodopsin

In spite of many still unsolved problems, the mechanism and energetics of the light-driven proton transport are now basically understood. Energy captured during photoexcitation, and retained in the form of bond rotations and strains of the retinal, is transformed into directed changes in the pKa values of vectorially arranged proton transfer groups. The framework for the spatial and temporal organization of these changes is provided by the protein near the retinal Schiff base. The transport is completed by proton transfer among three essential groups in three domains lying roughly parallel with the membrane plane (Fig. 1): (a) the anionic D85 that is included in a complex of residues on the extracellular side containing also R82, D212, Y57 and bound water; (b) the protonated Schiff base; and (c) the protonated D96 that is included in a complex of residues on the cytoplasmic side containing also R227, T46, S226, and bound water. Other neighboring polar groups and water bound elsewhere which play a role in the transport do so either by further influencing the pKa values of the three protonable groups, or by providing passive pathways for proton transfer. The Schiff base proton, destabilized after photoexcitation, is transferred to the low pKa group D85 located on the extracellular side. The access of the deprotonated Schiff base then changes to the cytoplasmic side (the 'reprotonation switch') and its proton affinity increases. Finally, the proton of the high pKa group D96, with access to the cytoplasmic side, is destabilized by a protein conformational change through rearrangement of R227, T46, S226 and bound water, and becomes transferred to the Schiff base. As shown schematically in Fig. 3, these internal events are coupled to proton release and uptake at the two aqueous surfaces. The charge of the extracellular hydrogen-bonded complex is redistributed upon protonation of D85, and if the pH is above the pKa of the complex a proton is released to the bulk. After reprotonation of the Schiff base the pKa of the cytoplasmic hydrogen-bonded complex is raised well above the pH, and D96 regains a proton from the bulk. If the pH is lower than the pKa of the extracellular complex the proton release is delayed until the end of the photocycle. In either sequence there is net transfer of a proton from the cytoplasmic to the extracellular phase. The transfer of excess free energy from the chromophore to the protein, and finally to the transported proton, is described by a characteristic thermodynamic cycle.(ABSTRACT TRUNCATED AT 400 WORDS)

Study of the photocycle and charge motions of the bacteriorhodopsin mutant D96N

Absorption kinetic and electric measurements were performed on oriented purple membranes of D96N bacteriorhodopsin mutant embedded in polyacrylamide gel and the kinetic parameters of the photointermediates determined. The rate constants, obtained from fits to time-dependent concentrations, were used to calculate the relative electrogenicity of the intermediates. The signals were analyzed on the basis of different photocycle models. The preferred model is the sequential one with reversible reaction. To improve the quality of the fits the necessity of introducing a second L intermediate arose. We also attempted to interpret our data in the view of reversible reactions containing two parallel photocycles, but the pH dependencies of the rate constants and electrogenicities favored the model containing sequential reversible transitions. A fast equilibrium for the L2<==>M1 transition and a strong pH dependence of the M2 electrogenicity was found, indicating that the M1 to M2 transition involves complex charge motions, as is expected in a conformational change of the protein.

Relationship of proton uptake on the cytoplasmic surface and reisomerization of the retinal in the bacteriorhodopsin photocycle: an attempt to understand the complex kinetics of the pH changes and the N and O intermediates

In the bacteriorhodopsin photocycle the recovery of the initial BR state from the M intermediate occurs via the N and O intermediates. The molecular events in this process include reprotonation of the Schiff base and the subsequent uptake of a proton from the cytoplasmic side, as well as reisomerization of the retinal from 13-cis to all-trans. We have studied the kinetics of the intermediates and the proton uptake. At moderately low pH little of the N state accumulates, and the O state dominates in the reactions that lead from M to BR. The proton uptake lags behind the formation of O, suggesting the sequence N(0)<==>O(0) + H+ (from the bulk)-->O(+1)-->BR+H+ (to the bulk), where the superscripts indicate the net protonation state of the protein relative to BR. Together with a parallel study of ours at moderately high pH, these results suggest that the sequence of proton uptake and retinal reisomerization depends on pH: at low pH the isomerization occurs first and O accumulates, but at high pH the isomerization is delayed and therefore N accumulates. Although this model contains too many rate constants for rigorous testing, we find that it will generate most of the characteristic pH-dependent kinetic features of the photocycle with few assumptions other than pH dependency for protonation at the proton release and uptake steps.

Photoreaction of the N intermediate of bacteriorhodopsin, and its relationship to the decay kinetics of the M intermediate

Because the M photointermediate of recombinant T46V bacteriorhodopsin decays more rapidly and the N intermediate more slowly than in wild-type, the photoreaction of N could be examined without interference from M. We found that between pH 6 and 9 the photoproducts of N included both earlier suggested M-like intermediate and red-shifted R state. However, when the photoexcitation of N was at wavelengths below 500 nm the amount of M-like product decreased with increasing pH, and at pH 9 virtually only R was produced. In the dark, T46V contains an N-like conformer, in increasing amounts with increasing pH like wild-type but in 4-5 times greater concentrations. The photoreaction of this thermally produced state is much like that of the N intermediate. It is associated with the appearance of a slowly decaying M, but we calculate that under most conditions used to follow M in the wild-type photocycle the amount of N-like conformer, and therefore the amplitude of this slow component, will not be significant. The results confirm the suggestion [Fukuda & Kouyama (1992) Biochemistry 31, 11740-11747] that an M-like state is included among the photoproducts of N, but at the same time provide support to photocycle models in which the slow component of the biphasic M decay is attributed not to this secondary photoreaction or to a separate photocycle originating from a heterogeneous initial state, but to thermal equilibration between M and N in a single photocycle.

Light-induced reorientation in the purple membrane

Reorientation of bacteriorhodopsin in the native purple membrane was studied by time-resolved linear dichroism spectroscopy (TRLD) over the millisecond time regime. The time responses observed in TRLD are distinctly different from the isotropic transient absorption (TA) at wavelengths in the range 550-590 nm, where the bacteriorhodopsin ground state absorbs. In contrast, the TA and TRLD responses have nearly identical time dependence at 410 and 690 nm, where the intermediates M and O, respectively, principally contribute. These results demonstrate ground-state bacteriorhodopsin reorientation triggered by the photocycle. The TRLD and TA data are analyzed to test models for reorientational motion. Rotational diffusion of ground-state bacteriorhodopsin cannot account for the details of the data. Rather, the results are shown to be consistent with a reversible reorientation of "spectator" (nonexcited) members of the bacteriorhodopsin trimer in the purple membrane in response to the photocycling member of the trimer. This response may be associated with cooperativity in the trimer.

Pathways of proton transfer in the light-driven pump bacteriorhodopsin

The mechanism of proton transport in the light-driven pump bacteriorhodopsin is beginning to be understood. Light causes the all-trans to 13-cis isomerization of the retinal chromophore. This sets off a sequential and directed series of transient decreases in the pKa's of a) the retinal Schiff base, b) an extracellular proton release complex which includes asp-85, and c) a cytoplasmic proton uptake complex which includes asp-96. The timing of these pKa changes during the photoreaction cycle causes sequential proton transfers which result in the net movement of a proton across the protein, from the cytoplasmic to the extracellular surface.

Proton transfer from Asp-96 to the bacteriorhodopsin Schiff base is caused by a decrease of the pKa of Asp-96 which follows a protein backbone conformational change

In the bacteriorhodopsin photocycle the transported proton crosses the major part of the hydrophobic barrier during the M to N reaction; in this step the Schiff base near the middle of the protein is reprotonated from D96 located near the cytoplasmic surface. In the recombinant D212N protein at pH > 6, the Schiff base remains protonated throughout the photocycle [Needleman, Chang, Ni, Váró, Fornés, White, & Lanyi (1991) J. Biol. Chem. 266, 11478-11484]. Time-resolved difference spectra in the visible and infrared are described by the kinetic scheme BR-->K<==>L<==>N (-->N')-->BR. As evidenced by the large negative 1742-cm-1 band of the COOH group of the carboxylic acid, deprotonation of D96 in the N state takes place in spite of the absence of the unprotonated Schiff base acceptor group of the M intermediate. Instead of internal proton transfer to the Schiff base, the proton is released to the bulk, and can be detected with the indicator dye pyranine during the accumulation of N'. The D212N/D96N protein has a similar photocycle, but no proton is released. As in wild-type, deprotonation of D96 in the N state is accompanied by a protein backbone conformational change indicated by characteristic amide I and II bands. In D212N the residue D96 can thus deprotonate independent of the Schiff base, but perhaps dependent on the detected protein conformational change. This could occur through increased charge interaction between D96 and R227 and/or increased hydration near D96. We suggest that the proton transfer from D96 to the Schiff base in the wild-type photocycle is driven also by such a decrease in the pKa of D96.

Gene replacement in Halobacterium halobium and expression of bacteriorhodopsin mutants

A gene replacement method has been developed to express bacteriorhodopsin mutants in the archaeon Halobacterium halobium. Selectable plasmids carrying the bacterioopsin gene (bop) were integrated at the chromosomal bop locus of H. halobium. Under nonselective conditions, recombinants were isolated that had lost the integrated plasmid and retained a single chromosomal copy of the bop gene. This approach was used to construct a bop deletion strain. By using this strain, recombinants were obtained that express wild-type bacteriorhodopsin and mutants known to be defective in proton translocation. The expressed proteins were purified in a membrane fraction similar to purple membrane and were characterized in this form. UV/visible spectra of dark- and light-adapted bacteriorhodopsin from wild-type and Asp-96 mutants were identical to those of purple membrane. Arg-82, Asp-85, and Asp-212 mutants had 10- to 50-nm red shifts in their absorption maxima and showed altered light adaptation. The proton translocation activity of the wild-type samples and purple membrane was comparable, whereas the mutants had 0-60% of wild-type activity. These results support earlier studies of proton translocation mutants expressed in Escherichia coli.

Mechanism of light-dependent proton translocation by bacteriorhodopsin

Site-specific mutagenesis has identified amino acids involved in bR proton transport. Biophysical studies of the mutants have elucidated the roles of two membrane-embedded residues: Asp-85 serves as the acceptor for the proton from the isomerized retinylidene Schiff base, and Asp-96 participates in reprotonation of this group. The functions of Arg-82, Leu-93, Asp-212, Tyr-185, and other residues that affect bR properties when substituted are not as well understood. Structural characterization of the mutant proteins will clarify the effects of substitutions at these positions. Current efforts in the field remain directed at understanding how retinal isomerization is coupled to proton transport. In particular, there has been more emphasis on determining the structures of bR and its photointermediates. Since well-ordered crystals of bR have not been obtained, continued electron diffraction studies of purple membrane offer the best opportunity for structure refinement. Other informative techniques include solid-state nuclear magnetic resonance of isotopically labeled bR (56) and electron paramagnetic resonance of bR tagged with nitroxide spin labels (2, 3, 13, 15). Site-directed mutagenesis will be essential in these studies to introduce specific sites for derivatization with structural probes and to slow the decay of intermediates. Thus, combining molecular biology and biophysics will continue to provide solutions to fundamental problems in bR.

Deriving the intermediate spectra and photocycle kinetics from time-resolved difference spectra of bacteriorhodopsin. The simpler case of the recombinant D96N protein

The bacteriorhodopsin photocycle contains more than five spectrally distinct intermediates, and the complexity of their interconversions has precluded a rigorous solution of the kinetics. A representation of the photocycle of mutated D96N bacteriorhodopsin near neutral pH was given earlier (Váró, G., and J. K. Lanyi. 1991. Biochemistry. 30:5008-5015) as BRhv-->K<==>L<==>M1-->M2--> BR. Here we have reduced a set of time-resolved difference spectra for this simpler system to three base spectra, each assumed to consist of an unknown mixture of the pure K, L, and M difference spectra represented by a 3 x 3 matrix of concentration values between 0 and 1. After generating all allowed sets of spectra for K, L, and M (i.e., M1 + M2) at a 1:50 resolution of the matrix elements, invalid solutions were eliminated progressively in a search based on what is expected, empirically and from the theory of polyene excited states, for rhodopsin spectra. Significantly, the average matrix values changed little after the first and simplest of the search criteria that disallowed negative absorptions and more than one maximum for the M intermediate. We conclude from the statistics that during the search the solutions strongly converged into a narrow region of the multidimensional space of the concentration matrix. The data at three temperatures between 5 and 25 degrees C yielded a single set of spectra for K, L, and M; their fits are consistent with the earlier derived photocycle model for the D96N protein.