Active site lysine backbone undergoes conformational changes in the bacteriorhodopsin photocycle

Structural changes due to the deprotonation of the proton release group in the M-photointermediate of bacteriorhodopsin as revealed by time-resolved FTIR spectroscopy

One of the steps in the proton pumping cycle of bacteriorhodopsin (BR) is the release of a proton from the proton-release group (PRG) on the extracellular side of the Schiff base. This proton release takes place shortly after deprotonation of the Schiff base (L-to-M transition) and results in an increase in the pKa of Asp85, which is a crucial mechanistic step for one-way proton transfer for the entire photocycle. Deprotonation of the PRG can also be brought about without photoactivation, by raising the pH of the enzyme (pKa of PRG; approximately 9). Thus, comparison of the FTIR difference spectrum for formation of the M intermediate (M minus initial unphotolyzed BR state) at pH 7 to the corresponding spectrum generated at pH 10 may reveal structural changes specifically associated with deprotonation of the PRG. Vibrational bands of BR that change upon M formation are distributed across a broad region between 2120 and 1685 cm(-1). This broad band is made up of two parts. The band above 1780 cm(-1), which is insensitive to C15-deuteration of the retinal, may be due to a proton delocalized in the PRG. The band between 1725 and 1685 cm(-1), on the lower frequency side of the broad band, is sensitive to C15-deuteration. This band may arise from transition dipole coupling of the vibrations of backbone carbonyl groups in helix G with the side chain of Tyr57 and with the C15H of the Schiff base. In M, these broad bands are abolished, and the 3657 cm(-1) band, which is due to the disruption of the hydrogen bonding of a water molecule, probably with Arg82, appears. Loss of the interaction of the backbone carbonyl groups in helix G with Tyr57 and the Schiff base, and separation of Tyr57 from Arg82, may be causes of these spectral changes, leading to the stabilization of the protonated Asp85 in M.

Time-resolved microspectroscopy on a single crystal of bacteriorhodopsin reveals lattice-induced differences in the photocycle kinetics

The determination of the intermediate state structures of the bacteriorhodopsin photocycle has lead to an unprecedented level of understanding of the catalytic process exerted by a membrane protein. However, the crystallographic structures of the intermediate states are only relevant if the working cycle is not impaired by the crystal lattice. Therefore, we applied visible and Fourier transform infrared spectroscopy (FTIR) microspectroscopy with microsecond time resolution to compare the photoreaction of a single bacteriorhodopsin crystal to that of bacteriorhodopsin residing in the native purple membrane. The analysis of the FTIR difference spectra of the resolved intermediate states reveals great similarity in structural changes taking place in the crystal and in PM. However, the kinetics of the photocycle are significantly altered in the three-dimensional crystal as compared to PM. Strikingly, the L state decay is accelerated in the crystal, whereas the M decay is delayed. The physical origin of this deviation and the implications for trapping of intermediate states are discussed. As a methodological advance, time-resolved step-scan FTIR spectroscopy on a single protein crystal is demonstrated for the first time which may be used in the future to gauge the functionality of other crystallized proteins with the molecular resolution of vibrational spectroscopy.

Crystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix

Structural changes in the proton pumping cycle of wild-type bacteriorhodopsin were investigated by using a 3D crystal (space group P622)prepared by the membrane fusion method. Protein-protein contacts in the crystal elongate the lifetime of the M intermediate by a factor of approximately 100,allowing high levels of the M intermediate to accumulate under continuous illumination. When the M intermediate generated at room temperature was exposed to a low flux of X-rays (approximately 10(14) photons/mm2), this yellow intermediate was converted into a blue species having an absorption maximum at 650 nm. This color change is suggested to accompany a configuration change in the retinal-Lys216 chain. The true conformational change associated with formation of the M intermediate was analyzed by taking the X-radiation-induced structural change into account. Our result indicates that, upon formation of the M intermediate, helix G move stowards the extra-cellular side by, on average, 0.5 angstroms. This movement is coupled with several reactions occurring at distal sites in the protein: (1) reorientation of the side-chain of Leu93 contacting the C13 methyl group of retinal, which is accompanied by detachment of a water molecule from the Schiff base; (2) a significant distortion in the F-G loop, triggering destruction of a hydrogen bonding interaction between a pair of glutamate groups (Glu194 and Glu204); (3) formation of a salt bridge between the carboxylate group of Glu204 and the guanidinium ion of Arg82, which is accompanied by a large distortion in the extra-cellular half of helix C; (4)noticeable movements of the AB loop and the cytoplasmic end of helix B. But, no appreciable change is induced in the peptide backbone of helices A,D, E and F. These structural changes are discussed from the viewpoint of translocation of water molecules.

Structural and mechanistic insight from high resolution structures of archaeal rhodopsins

Lipidic cubic phase-grown crystals yielded high resolution structures of a number of archaeal retinal proteins, the molecular mechanisms of which are being revealed as structures of photocycle intermediates become available. The structural basis for bacteriorhodopsin's mechanism of proton pumping is discussed, revealing a well-synchronized sequence of molecular events. Comparison with the high resolution structures of the halide pump halorhodopsin, as well as with the receptor sensory rhodopsin II, illustrates how small and localized structural changes result in functional divergence. Fundamental principles of energy transduction and sensory reception in the archaeal rhodopsins, which may have relevance to other systems, are discussed.

Deformation of Helix C in the Low Temperature L-intermediate of Bacteriorhodopsin

X-ray and electron diffraction studies of specific reaction intermediates, or reaction intermediate analogues, have produced a consistent picture of the structural mechanism of light-driven proton pumping by bacteriorhodopsin. Of central importance within this picture is the structure of the L-intermediate, which follows the retinal all-trans to 13-cis photoisomerization step of the K-intermediate and sets the stage for the primary proton transfer event from the positively charged Schiff base to the negatively charged Asp-85. Here we report the structural changes in bacteriorhodopsin following red light illumination at 150 K. Single crystal microspectrophotometry showed that only the L-intermediate is populated in three-dimensional crystals under these conditions. The experimental difference Fourier electron density map and refined crystallographic structure were consistent with those previously presented (Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2000) Nature 406, 645-648; Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2001) Photochem. Photobiol. 74, 794-804). Based on the refined crystallographic structures, molecular dynamic simulations were used to examine the influence of the conformational change of the protein that is associated with the K-to-L transition on retinal dynamics. Implications regarding the structural mechanism for proton pumping by bacteriorhodopsin are discussed.

Bacteriorhodopsin: a high-resolution structural view of vectorial proton transport

Recent 3-D structures of several intermediates in the photocycle of bacteriorhodopsin (bR) provide a detailed structural picture of this molecular proton pump in action. In this review, we describe the sequence of conformational changes of bR following the photoisomerization of its all-trans retinal chromophore, which is covalently bound via a protonated Schiff base to Lys216 in helix G, to a 13-cis configuration. The initial changes are localized near the protein's active site and a key water molecule is disordered. This water molecule serves as a keystone for the ground state of bR since, within the framework of the complex counter ion, it is important both for stabilizing the structure of the extracellular half of the protein, and for maintaining the high pK(a) of the Schiff base (the primary proton donor) and the low pK(a) of Asp85 (the primary proton acceptor). Subsequent structural rearrangements propagate out from the active site towards the extracellular half of the protein, with a local flex of helix C exaggerating an early movement of Asp85 towards the Schiff base, thereby facilitating proton transfer between these two groups. Other coupled rearrangements indicate the mechanism of proton release to the extracellular medium. On the cytoplasmic half of the protein, a local unwinding of helix G near the backbone of Lys216 provides sites for water molecules to order and define a pathway for the reprotonation of the Schiff base from Asp96 later in the photocycle. A steric clash of the photoisomerized retinal with Trp182 in helix F drives an outward tilt of the cytoplasmic half of this helix, opening the proton transport channel and enabling a proton to be taken up from the cytoplasm. Although bR is the first integral membrane protein to have its catalytic mechanism structurally characterized in detail, several key results were anticipated in advance of the structural model and the general framework for vectorial proton transport has, by and large, been preserved.

Early structural rearrangements in the photocycle of an integral membrane sensory receptor

Sensory rhodopsins are the primary receptors of vision in animals and phototaxis in microorganisms. Light triggers the rapid isomerization of a buried retinal chromophore, which the protein both accommodates and amplifies into the larger structural rearrangements required for signaling. We trapped an early intermediate of the photocycle of sensory rhodopsin II from Natronobacterium pharaonis (pSRII) in 3D crystals and determined its X-ray structure to 2.3 A resolution. The observed structural rearrangements were localized near the retinal chromophore, with a key water molecule becoming disordered and the retinal's beta-ionone ring undergoing a prominent movement. Comparison with the early structural rearrangements of bacteriorhodopsin illustrates how modifications in the retinal binding pocket of pSRII allow subtle differences in the early relaxation of photoisomerized retinal.

Retinal isomerization in bacteriorhodopsin is controlled by specific chromophore-protein interactions. A study with noncovalent artificial pigments

It has previously been shown that, in mutants lacking the Lys-216 residue, protonated Schiff bases of retinal occupy noncovalently the bacteriorhodopsin (bR) binding site. Moreover, the retinal-Lys-216 covalent bond is not a prerequisite for initiating the photochemical and proton pump activity of the pigment. In the present work, various Schiff bases of aromatic polyene chromophores were incubated with bacterioopsin to give noncovalent pigments that retain the Lys-216 residue in the binding site. It was observed that the pigment's absorption was considerably red-shifted relative to the corresponding protonated Schiff bases (PSB) in solution and was sensitive to Schiff base linkage substitution. Their PSB pK(a) is considerably elevated, similarly to those of related covalently bound pigments. However, the characteristic low-pH purple to blue transition is not observed, but rather a chromophore release from the binding site takes place that is characterized by a pK(a) of approximately 6 (sensitive to the specific complex). It is suggested that, in variance with native bR, in these complexes Asp-85 is protonated and Asp-212 serves as the sole negatively charged counterion. In contrast to the bound analogues, no photocycle could be detected. It is suggested that a specific retinal-protein geometrical arrangement in the binding site is a prerequisite for achieving the selective retinal photoisomerization.

Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin

A wide variety of mechanisms are used to generate a proton-motive potential across cell membranes, a function lying at the heart of bioenergetics. Bacteriorhodopsin, the simplest known proton pump, provides a paradigm for understanding this process. Here we report, at 2.1 A resolution, the structural changes in bacteriorhodopsin immediately preceding the primary proton transfer event in its photocycle. The early structural rearrangements propagate from the protein's core towards the extracellular surface, disrupting the network of hydrogen-bonded water molecules that stabilizes helix C in the ground state. Concomitantly, a bend of this helix enables the negatively charged primary proton acceptor, Asp 85, to approach closer to the positively charged primary proton donor, the Schiff base. The primary proton transfer event would then neutralize these two groups, cancelling their electrostatic attraction and facilitating a relaxation of helix C to a less strained geometry. Reprotonation of the Schiff base by Asp 85 would thereby be impeded, ensuring vectorial proton transport. Structural rearrangements also occur near the protein's surface, aiding proton release to the extracellular medium.

Coupling photoisomerization of retinal to directional transport in bacteriorhodopsin

In order to understand how isomerization of the retinal drives unidirectional transmembrane ion transport in bacteriorhodopsin, we determined the atomic structures of the BR state and M photointermediate of the E204Q mutant, to 1.7 and 1.8 A resolution, respectively. Comparison of this M, in which proton release to the extracellular surface is blocked, with the previously determined M in the D96N mutant indicates that the changes in the extracellular region are initiated by changes in the electrostatic interactions of the retinal Schiff base with Asp85 and Asp212, but those on the cytoplasmic side originate from steric conflict of the 13-methyl retinal group with Trp182 and distortion of the pi-bulge of helix G. The structural changes suggest that protonation of Asp85 initiates a cascade of atomic displacements in the extracellular region that cause release of a proton to the surface. The progressive relaxation of the strained 13-cis retinal chain with deprotonated Schiff base, in turn, initiates atomic displacements in the cytoplasmic region that cause the intercalation of a hydrogen-bonded water molecule between Thr46 and Asp96. This accounts for the lowering of the pK(a) of Asp96, which then reprotonates the Schiff base via a newly formed chain of water molecules that is extending toward the Schiff base.

High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle

Bacteriorhodopsin is the simplest known photon-driven proton pump and as such provides a model for the study of a basic function in bioenergetics. Its seven transmembrane helices encompass a proton translocation pathway containing the chromophore, a retinal molecule covalently bound to lysine 216 through a protonated Schiff base, and a series of proton donors and acceptors. Photoisomerization of the all-trans retinal to the 13-cis configuration initiates the vectorial translocation of a proton from the Schiff base, the primary proton donor, to the extracellular side, followed by reprotonation of the Schiff base from the cytoplasm. Here we describe the high-resolution X-ray structure of an early intermediate in the photocycle of bacteriorhodopsin, which is formed directly after photoexcitation. A key water molecule is dislocated, allowing the primary proton acceptor, Asp 85, to move. Movement of the main-chain Lys 216 locally disrupts the hydrogen-bonding network of helix G, facilitating structural changes later in the photocycle.

Conformational change of helix G in the bacteriorhodopsin photocycle: investigation with heavy atom labeling and x-ray diffraction

According to the current structural model of bacteriorhodopsin, Ile222 is located at the cytoplasmic end of helix G. We labeled the single cysteine of the site-directed mutant Ile222 --> Cys with p-chloromercuribenzoic acid and determined the position of the labeled mercury by x-ray diffraction in the unphotolyzed state, and in the MN photointermediate accumulated in the presence of guanidine hydrochloride at pH 9.5. According to the difference Fourier maps between the MN intermediate and the unphotolyzed state, the structural change in the MN intermediate was not affected by mercury labeling. The difference Fourier map between the labeled and the unlabeled I222C gave the position of the mercury label. This information was obtained for both the unphotolyzed state and the MN intermediate. We found that the position of the mercury at residue 222 is shifted by 2.1 +/- 0.8 A in the MN intermediate. This agrees with earlier results that suggested a structural change in the G helix. The movement of the mercury label is so large that it must originate from a cooperative conformational change in the helix G at its cytoplasmic end, rather than from displacement of residue 222. Because Ile222 is located at the same level on the z coordinate as Asp96, the structural change in the G helix could have the functional role of perturbing the environment and therefore the pKa of this functionally important aspartate.

X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases

Lipidic cubic phases provide a continuous three-dimensional bilayer matrix that facilitates nucleation and growth of bacteriorhodopsin microcrystals. The crystals diffract x-rays isotropically to 2.0 angstroms. The structure of this light-driven proton pump was solved at a resolution of 2.5 angstroms by molecular replacement, using previous results from electron crystallographic studies as a model. The earlier structure was generally confirmed, but several differences were found, including loop conformations and side chain residues. Eight water molecules are now identified experimentally in the proton pathway. These findings reveal the constituents of the proton translocation pathway in the ground state.

Structural dynamics of water and the peptide backbone around the Schiff base associated with the light-activated process of octopus rhodopsin

Difference Fourier transform infrared spectra were recorded for the formation of the photointermediates and isorhodopsin from octopus rhodopsin at low temperatures. Analysis was done for H bonding of the Schiff base, internal water molecules, and the peptide backbone. The imine hydrogen of the Schiff base was in the same H bonding state throughout the photointermediates and the unphotolyzed state. In contrast, H bonding of the hydrogen of the water molecule whose oxygen might be complexed with the imine hydrogen of the Schiff base was altered upon the formation of bathorhodopsin. The same water molecule was in a different H bonding state in the subsequent intermediates, lumirhodopsin and mesorhodopsin. These intermediates were also characterized by a decrease in the C = N bond order of the Schiff base as a reflection of distorted structure around the Schiff base. The polar N-H bond in these intermediates could be also ascribed to the Schiff base. Some changes in H bonding of water and the perturbation of the polyene chain in lumirhodopsin and mesorhodopsin were also observed in isorhodopsin. Acid metarhodopsin exhibited extensive changes in the H bonding states of the peptide backbone and internal water molecules. A large part of these changes was extinguished in alkaline metarhodopsin with the unprotonated Schiff base, suggesting interaction of the protonated Schiff base with the peptide backbone and intramembrane water molecules in acid metarhodopsin.

Structural changes in the peptide backbone in complex formation between activated rhodopsin and transducin studied by FTIR spectroscopy

Structural changes in the complex formation between transducin and metarhodopsin II, the activated form of photolyzed rhodopsin, in visual transduction processes were analyzed by Fourier transform infrared spectroscopy. The spectrum of the complex was obtained by subtracting the contribution of metarhodopsin I and uncomplexed metarhodopsin II. The averaged spectrum upon the complex formation was then compared with that in the conversion of rhodopsin-to-metarhodopsin II. Frequency shifts of the peptide carbonyl vibrations at 1686, 1674, and 1661 cm-1 to 1640 cm-1 were observed upon complex formation from metarhodopsin II plus transducin. These changes must have resulted from the strengthening of H-bonding of one or a few peptide groups but is not ascribable to global conformation change. Changes in the frequencies of the peptide amides were also detected. With regard to intramembrane carboxylic acid residues, no further changes were noticed in the carboxyl vibrations of Asp83, Glu122, and Glu113. Only a small change possibly due to Glu134 was detected.

A three-dimensional difference map of the N intermediate in the bacteriorhodopsin photocycle: part of the F helix tilts in the M to N transition

The N intermediate of the bacteriorhodopsin photocycle was trapped for electron diffraction studies in glucose-embedded specimens of the site-directed mutant Phe219 --> Leu. At neutral pH, the N-bR difference Fourier transform infrared spectrum of this mutant is indistinguishable from published difference spectra obtained for wild-type bacteriorhodopsin at alkaline pH. An electron diffraction difference map of the N intermediate in projection shows large differences near the F and the G helix, which are very similar to the features seen in the M intermediates of the Asp96 --> Gly mutant [Subramaniam et al. (1993) EMBO J. 12, 1-8]. This similarity was anticipated on the basis of Fourier transform infrared data, which have shown that the M intermediate trapped in Asp96 mutants already has the protein structure of the N intermediate [Sasaki et al. (1992) J. Biol. Chem. 267, 20782-20786]. A preliminary three-dimensional difference map of the N intermediate, calculated from electron diffraction data of samples tilted at 25 degrees, clearly shows that the change on the F helix consists of an outward movement of the cytoplasmic end of the helix. In addition, the cytoplasmic side of the G helix moves or becomes more ordered. Comparison with published difference maps of the M intermediate indicates that the F helix tilt occurs in the M to N transition, but the G helix change represents an earlier step in the photocycle.

Hydrogen bonds of water and C==O groups coordinate long-range structural changes in the L photointermediate of bacteriorhodopsin

Fourier transform infrared spectra of light-adapted bacteriorhodopsin exhibit a band at 1618 cm(-1) that shifts to 1625 cm(-1) upon formation of the L intermediate. It is assigned to the peptide C==O of Val49 from the fact that it shifts in [1-(13)C]valine-labeled bacteriorhodopsin and appears perturbed in the Val49-->Met mutant. The intensity of the BR-->L difference band is reduced in the Thr46-->Val mutant but restored by the additional mutation of Asp96-->Asn. These intensity changes are closely correlated with the H-bonding change of water olecules, suggesting that the peptide C==O of Val49 is hydrated. This could arise in the Thr46-->Val mutant because of perturbation of the C==O of Val46, which points toward Val49. The Val49-->Ala mutation influences a peptide N-H, presumably of Val49, and the carboxylic C==O of Asp96, as well as water molecules proximal to Asp85. Conversely, the water molecule assumed to be in the cavity that arises from the missing two methyl groups in V49A could be affected in the mutant of Asp96-->Asn. We propose that the perturbation exerted on Asp85 by the Schiff base in the L intermediate is transmitted to Asp96 through H-bonding of water molecules in the Asp85-Val49 region, the C==O of Val49, H-bonding between Val49 and Thr46, and H-bonding between Thr46 and Asp96.