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Hydration switch model for the proton transfer in the Schiff base region of bacteriorhodopsin
Biochimica et Biophysica Acta 1658 (2004) 72 – 79 www.bba-direct.com
Review
Hydration switch model for the proton transfer in the Schiff base region of bacteriorhodopsin Hideki Kandori * Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan Received 18 February 2004; received in revised form 15 March 2004; accepted 15 March 2004 Available online 15 June 2004
Abstract In a light-driven proton-pump protein, bacteriorhodopsin (BR), protonated Schiff base of the retinal chromophore and Asp85 form ionpair state, which is stabilized by a bridged water molecule. After light absorption, all-trans to 13-cis photoisomerization takes place, followed by the primary proton transfer from the Schiff base to Asp85 that triggers sequential proton transfer reactions for the pump. Fourier transform infrared (FTIR) spectroscopy first observed O – H stretching vibrations of water during the photocycle of BR, and accurate spectral acquisition has extended the water stretching frequencies into the entire stretching frequency region in D2O. This enabled to capture the water molecules hydrating with negative charges, and we have identified the water O – D stretch at 2171 cm 1 as the bridged water interacting with Asp85. We found that retinal isomerization weakens the hydrogen bond in the K intermediate, but not in the later intermediates such as L, M, and N. On the basis of the observation particularly on the M intermediate, we proposed a model for the mechanism of proton transfer from the Schiff base to Asp85. In the ‘‘hydration switch model’’, hydration of a water molecule is switched in the M intermediate from Asp85 to Asp212. This will have raised the pKa of the proton acceptor, and the proton transfer is from the Schiff base to Asp85. D 2004 Elsevier B.V. All rights reserved. Keywords: Proton pump; Retinal; Hydrogen bond; Fourier transform infrared spectroscopy; Internal water molecule; Isotope effect
1. Introduction Proteins that actively pump protons across membranes must translocate them through hydrophobic regions inside the protein. Therefore, internal water molecules are presumed to play a crucial role in active proton transport [1]. The water must participate in hydrogen-bonding networks inside proteins that constitute proton pathways. Nevertheless, the proton pathways cannot be fully connected between the two sides of the membrane, because the proton gradient formed will be collapsed. This is an important aspect in distinguishing pumps from channels. The former needs a ‘switch’, which ensures the vectoriality of the pumping. Besides participating in hydrogen-bonding networks, water molecules may be elements of the switch, which mediates an essential proton transfer at the active site. While little is known about the structure and function of internal water
* Fax: +81-52-735-5207. E-mail address: [email protected] (H. Kandori). 0005-2728/$ - see front matter D 2004 Elsevier B.V. All rights reserved. doi:10.1016/j.bbabio.2004.03.015
molecules in such proteins generally, the greatest progress has been made in bacteriorhodopsin (BR). BR is a light-driven proton pump in Halobacterium salinarum that contains all-trans retinal as chromophore (Fig. 1) [2,3]. The retinal binds covalently to Lys216 through a protonated Schiff base. Upon light absorption, photoisomerization takes place from the all-trans to 13-cis form in subpicoseconds, followed by a cyclic reaction that comprises a series of intermediates, designated as the J, K, L, M, N, and O states. Proton pump in BR is achieved by five proton transfer reactions shown in Fig. 1. The primary proton transfer from the Schiff base to Asp85 (1) and the proton release from the groups containing Glu204 and Glu194 (2) occur in the L – M transition of the BR photocycle at neutral pH. The M– N transition accompanies a proton transfer from Asp96 to the Schiff base (3), while the proton uptake occurs in the N –O transition (4). Finally, the proton transfer from Asp85 to the extracellular proton release group takes place in the O – BR transition (5). Although proton transfer reactions inside protein are spatially and temporally well controlled, mutation studies
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and at Arg82, and counterbalancing negative charges located at Asp85 and Asp212 (Fig. 2) [6,7]. The quadrupole inside protein is stabilized by three water molecules (water401, 402, and 406), which constitute a roughly planar pentagonal cluster together with one oxygen each of Asp85 and Asp212. A notable structural feature is that Asp85 and Asp212 are located at similar distances from the retinal Schiff base, whereas the Schiff base proton is transferred only to Asp85 (Fig. 2). The mechanism of the proton transfer from the Schiff base to Asp85 has therefore attracted much interest, and the water molecules in the Schiff base region presumably play important roles in the proton transfer reaction [1]. The Schiff base proton may be transferred through the proton wire formed between the donor (Schiff base) and acceptor (Asp85). On the other hand, it may directly jump between them. Another interesting hypothesis is that ‘‘proton transfer’’ is in fact hydroxide transfer, where a hydroxide (OH ) moves from the extracellular to the cytoplasmic domain as does for a chloride ion in the D85T mutant BR [8]. In any models, important are the intermediate structures before and after the proton transfer (the L and M intermediates, respectively). However, there are variations
Fig. 1. X-ray crystallographic structures of the Schiff base region in BR (PDB entry 1C3W) [6]. Proton pathways are viewed from A-helix, which is removed in the figure. Protonatable groups and bound water molecules are highlighted by stick drawing and green spheres, respectively. Numbers with arrows represent the sequence of proton transfer reactions.
have provided important information. The proton pumping activity is retained upon replacement of terminal protonatable groups such as Asp96, Glu204, and Glu194 [4]. Therefore, even though protons are transferred to and from Asp96 and Glu204 and/or Glu194 during the photocycle, these side chains cannot be actively involved in the switch. In contrast, there is no doubt that Asp85 is involved in the switch, because its replacement results in the loss of proton pumping ability [4]. Not only losing the proton pump function, the replacement of aspartate with threonine at position 85 can convert into a chloride pump like halorhodopsin [5]. Thus, the domain containing Asp85 and the retinal Schiff base is likely to constitute the switch, the heart of the pump. It is generally accepted that the primary proton transfer ensures the directionality in pump, because the accessibility is switched from the extracellular side to the cytoplasmic side, either upon the formation of M or the early-to-late M transition [2,3]. In the Schiff base region, there is a quadrupolar structure with positive charges located at the protonated Schiff base
Fig. 2. X-ray crystallographic structures of the Schiff base region in BR (PDB entry 1C3W) [6]. The membrane normal is approximately in the vertical direction of this figure. Upper and lower regions correspond to the cytoplasmic and extracellular sides, respectively. Green spheres (401, 402, and 406) represent water molecules which form a roughly pentagonal cluster with an oxygen from Asp85 and an oxygen from Asp212. Watercontaining pentagonal cluster structure will stabilize an electric quadrupole in this region. Hydrogen atoms and hydrogen bonds (dotted lines) are supposed from the structure, while the numbers are the hydrogen-bonding ˚ . After photoisomerization of the retinal, the Schiff base distances in A proton is transferred to Asp85 in the L-to-M transition (arrow), although two aspartates are located symmetrically.
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among the reported crystallographic structures of photointermediates. It should be emphasized that tiny difference in bond angle in retinal could lead to significant difference in the orientation of the N-H group of the Schiff base. Similar argument is possible for the positions of internal water molecules. A different approach to internal water molecules of BR is shown in this review article. Here I introduce our recent studies on the internal water molecules by means of Fourier transform infrared (FTIR) spectroscopy.1 Detection of internal water molecules under strong hydrogen bonds is one of recent highlights, and a model for the primary proton transfer reaction is proposed on the basis of such measurements.
2. FTIR studies of internal water molecules of BR 2.1. Detection of water in the primary reaction of BR FTIR spectroscopy of biological molecules is usually applied in the frequency region < 1800 cm 1, giving secondary structural information. Strong absorption of water molecules in the 3700 –3000 cm 1 region prevents from obtaining accurate spectra in the region. That is, information of internal water molecules is easily masked by solvent water molecules, as the latter are much more numerous. However, it is known that BR films exhibit a normal photocycle under suitable hydration conditions. In addition, BR being a photoreceptive protein, the protein conformation changes are conveniently obtained as difference IR spectra. These facts allowed to obtain difference IR spectra in the frequency region not only < 1800 cm 1, but also in the water stretching region. This author reviewed the details of the historical aspects of FTIR studies on BR in this journal 4 years ago [1]. O –H stretching vibrations of water molecules were identified by comparing hydrations of H2O and H218O. Then, various mutants have been tested for several intermediate states, which provided information on the location of bound water molecules to BR. As described in the review, however, there was a limitation in frequency for the previous FTIR measurements, where the observed frequency region of water molecules in the previous FTIR studies was limited in the >3450 cm 1 [1]. It is noted that the O – H stretching frequency is lowered when hydrogen bond is strengthened. This means that FTIR spectroscopy has been able to detect only the narrow region for rather free O – H groups, while information on the bridged water O – H through hydrogen bonding was not possible to obtain. The Schiff base structure in Fig. 2 suggests the importance to probe water 1
History of the study on internal water molecules of BR was reviewed in detail in the previous article [1]. The first FTIR study on water molecules was reported in 1992 by Maeda et al. [32]. Before the report, internal water molecules of BR were also discussed on the basis of resonance Raman spectroscopy [33], NMR spectroscopy [34], and neutron diffraction [35].
vibrations under strong hydrogen bonds. The reason for the difficulty in identifying water O –H bands in the lower frequency region is as follows: (i) the spectral accuracy is less because of intense absorption by water, (ii) many protein bands other than water O – H stretches overlap this region, and (iii) strongly hydrogen-bonded water possesses broad O –H stretching bands. These facts have disturbed observations of clear isotope shifts. In particular, an isotope shift between O – H and 18O – H is about 10 cm 1, and such small shift could be hidden in complex spectral features in the 3450 –3000-cm 1 region. About 6 years ago, we attempted to extend the frequency region of water stretching vibrations that monitor strong hydrogen bonds. By optimizing the measuring system of polarized FTIR spectroscopy, we could measure the K minus BR difference spectra in whole mid-infrared region (4000 – 700 cm 1) [9]. One of the key issues was to obtain the difference spectra in D2O, by which the D2O-insensitive stretching vibrations are separated in frequency. On the other hand, BR pumps deuterium in D2O, so that the O – H groups of internal water molecules that participate proton transport should be exchanged for O –D groups. We thus expected to observe the isotope shift even for the bridged water stretches. The K minus BR difference spectra in Fig. 3a indeed show the isotope shift of water not only for weak hydrogen bonds (2700 – 2500 cm 1), but also for strong hydrogen bonds ( < 2400 cm 1) [10]. There are at least six negative bands of water O –D stretches at 2690, 2636, 2599, 2323, 2292, and 2171 cm 1, indicating that retinal photoisomerization alters hydrogen bonds of several water molecules. Interestingly, the observed water bands were at 2700– 2600 and 2350 –2150 cm 1, locating at both edges in broad absorption spectra of D2O (gray spectra in Fig. 3). This fact suggests that these water molecules are specifically bound to protein. It is particularly noted that the O –D stretch at 2171 cm 1 is much lower in frequency than those for the fully hydrated tetrahedral water molecules, suggesting that the hydrogen bond acceptor of this water molecule is negatively charged, such as oxygens of Asp85 and Asp212 (Fig. 2) [10]. Fig. 3a shows that most bands in the 2700 – 2000 cm 1 region originate from water O – D stretches. On the other hand, some other bands have been already identified. We assigned the 2506 ( )/2466 (+) cm 1 bands as the O –D stretch of Thr89 by use of [3-18O]threonine-labeled BR sample [11]. Low frequency (2506 cm 1) as the threonine O – D stretch in BR indicates strong hydrogen bond of Thr89, which is consistent with the BR structure (Fig. 2). Lower frequency shift to 2466 cm 1 in K implies further strengthened hydrogen bond of Thr89 presumably with Asp85. We assigned the negative 2171 and 2123 cm 1 bands contain N –D stretch of the Schiff base by use of [s-15N]lysine-labeled BR sample [12]. The presence of the N –D stretch of the Schiff base at the same frequency as the O –D stretch of water is one of the reasons of small isotope
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1 Fig. 3. Difference IR spectra are compared between hydration with D2O (red lines) and D18 region. The window tilting 2 O (blue lines) in the 2750 – 1930 cm angles are 53.5j in the polarized IR measurements. The K minus BR (a), L minus BR (b), M minus BR (c) and N minus BR (d) spectra are measured at 77, 170, 230, and 273 K, respectively. The gray curve in the 2700 – 2000 cm 1 region represents O – D stretching vibrations of D2O. Green-labeled frequencies correspond to those identified as water stretching vibrations. Purple-labeled frequencies are O – D stretch of Thr89 [11,28], while the underlined-frequencies are N – D stretch of the Schiff base [12]. This figure is modified from Ref. [15].
shift of water for the 2171 cm 1 band (Fig. 3a). The ND stretch of the Schiff base appears at about 2466 cm 1 in the K intermediate, indicating that the hydrogen bond of the Schiff base is significantly weakened. Polarized measurements suggested that the N –D group of the Schiff base in K orients along the membrane [12]. Thus, Fig. 3a exhibits strong perturbation of the Schiff base region (Fig. 1) upon retinal photoisomerization through the analysis of stretching vibrations. 2.2. Assignment of the O –D stretch at 2171 cm
1
in BR
Since vibrational bands of water molecules are obtained, normal mode analysis is important on the basis of the BR structure (Fig. 2). In the same year of our IR study, Hayashi and Ohmine [13] reported the quantum mechanical and molecular mechanical (QM/MM) calculation of the Schiff base region in BR. According to their calculation, the water O – D stretch at the lowest frequency (2171 cm 1) corresponds to the stretching mode of water402 bound to Asp85, while another O – D stretch of water402 is about 350 cm 1 higher in frequency. This means that the hydrogen bond of water402 with Asp85 is much stronger than that with Asp212, even though it is not clear from Fig. 2. Stronger association with Asp85 may be related to the fact that Asp85 is the principal counterion of the protonated Schiff base. However, it should be noted that the 2171 cm 1 band has not been experimentally proven to be the O –D stretch of water402 interacting with Asp85. Therefore, we next measured the K minus BR spectra for various BR mutants [14].
If the 2171 cm 1 band originates from the O –D stretch of water402 hydrating Asp85, as predicted by Hayashi and Ohmine, removal of the negative charge at the position 85 by a mutation should significantly affect the band. Fig. 4b indeed shows that the broad negative feature in the 2300– 2000 cm 1 region does not exhibit the isotope shift in D85N. The negative band can be assigned as the N –D stretch of the Schiff base like in the wild type BR [12]. D85N lacks not only the 2171 cm 1 band, but also all water bands in this frequency region, suggesting the important role of the negative charge at the position 85. We also expected that the lack of the negative charge at the position 212 will not significantly affect the 2171 cm 1 band according to Hayashi and Ohmine. Nevertheless, Fig. 4c shows that all water bands disappear in the < 2400 cm 1 region in D212N. The results of both D85N and D212N imply the crucial role of each negative charge in the pentagonal cluster, leading to the possible assignment of the water bands at 2323, 2292, and 2171 cm 1 as the O –D stretches involved in the pentagonal cluster (Fig. 2). On the other hand, we could not establish that the 2171 cm 1 band originates from the O – D stretch of water402 hydrating Asp85. It seems that Asp85 and Asp212 are directly involved in the pentagonal cluster structure, so that their mutations greatly change the hydrogen bonding structure. Subsequently, we performed additional mutation studies. One oxygen atom of Asp85 and Asp212 is involved in the pentagonal cluster, while another oxygen forms a hydrogen bond with Thr89 and Tyr185, respectively (Fig. 2). Therefore, we expected that the cleavage of these hydrogen bonds
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molecules suggests that the hydrogen bonding interaction of water402 is stronger with Asp85 than with Asp212 [14]. Since the bridged water interacts more strongly with Asp85, Asp85 is presumably a stronger counterion than Asp212. The role of the negative charge on Asp212 is also crucial. If it is neutralized, all the bands of strongly hydrogen-bonded water molecules disappear (Fig. 2c). Thus, the pentagonal cluster structure composed of the two negative charges may be essential for the function of BR. In fact, D85N and D212N proteins do not pump protons, while mutants of Tyr185 and Thr89 do [4]. Measurements of various mutant proteins are in progress to test the hypothesis that ‘proton pump activity is correlated with the presence of internal water molecules under strongly hydrogen-bonded conditions’. 2.3. Hydration switch model
Fig. 4. The K minus BR difference infrared spectra of the wild type (a), D85N (b), D212N (c), Y185F (d), and T89A (e) BR in the 2380 – 2000 cm 1 region. The samples were hydrated with D2O (red lines) or D18 2 O (blue lines), and spectra were measured at 77 K. Labeled frequencies correspond to these bands identified as water stretching vibrations. This figure is modified from Ref. [14].
would localize the negative charges onto the respective oxygens of the pentagonal cluster. As a consequence, the 2171 cm 1 band would be further down-shifted in a mutant of Thr89, while it would not be much influenced in a mutant of Tyr185. That was indeed the case. Fig. 2d shows that the 2171 cm 1 band of water is preserved in the Y185F mutant, as well as the two positive and the two negative bands of water. On the other hand, a strong negative band appears at 2088 cm 1 in the T89A mutant, which exhibits lower frequency shift in D218O. The frequency change by >80 cm 1 in T89A, but not in Y185F, strongly supports the proposal by the QM/MM calculation that the 2171 cm 1 band originates from the O – D stretch of water402 [13]. The negative peak is present at 2166 and 2155 cm 1 in T89S and T89C, respectively, implying that the hydrogen-bonding interactions with Thr89 and water402 determine negative charge distribution between the side chain oxygens of Asp85 [14]. According to the X-ray structure of BR, Asp85 and Asp212 look symmetrical in the pentagonal cluster structure (Fig. 1). However, the FTIR study of internal water
Since the IR observations of the O – D stretch of water in their entire stretching vibrational frequencies provided new information on the water structural changes before and after retinal isomerization [10], their extension study for late photointermediates will lead to better understanding of water structural changes during proton pump of BR. Therefore, we measured the IR difference spectra in the water O – D stretching region of the L, M, and N intermediates. Fig. 3 shows that no isotope effect of water was observed in the < 2500 cm 1 region for the L minus BR (b), M minus BR (c), and N minus BR (d) spectra, being in clear contrast to the K minus BR (a) spectra [15]. Water stretching vibrations were only observed at >2500 cm 1. The negative band at 2690 cm 1 was commonly observed among all spectra, and the previous mutation studies for the O – H stretching region revealed that the location of the water molecule is near Asp85 [1]. The L minus BR spectrum exhibits the additional negative water band at 2669 cm 1, while broad positive feature due to water appeared in the 2650– 2560 cm 1 region (Fig. 3b), whose locations were estimated to be at the cytoplasmic region [1]. The M minus BR spectrum exhibits the positive water bands at 2715 and 2640 cm 1, whose locations were suggested to be at the cytoplasmic region [1]. Unlike in K, we did not observe spectral changes of the water bands under strong hydrogen-bonding conditions in L, M, and N (Fig. 3). It is particularly noted that the 2171 cm 1 band as the O – D stretch of water402 hydrating with Asp85 was not observed for the L minus BR and M minus BR spectra. On the basis of these IR observations, we interpreted the proton transfer mechanism from the Schiff base to Asp85 as follows. In BR, the O – D stretch of water402 bound to Asp85 is at 2171 cm 1 (Fig. 5). Upon photoisomerization, the N – D group of the Schiff base displaces to form parallel orientation to the membrane [12]. As a consequence, the water-containing pentagonal cluster structure is perturbed, and the interaction between water402 and Asp85 is weakened (Fig. 5). Such structural change possibly involves rotational motion of water402
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Fig. 5. Hydration switch model as the proton transfer mechanism from the Schiff base to Asp85. Structure of the Schiff base region in D2O is schematically drawn. Strong hydrogen bond of water402, whose O – D stretch appears at 2171 cm 1, is highlighted in BR, L, and M. The acceptor is Asp85 in BR and L, while being switched to Asp212 in M. In this model, hydration switch of water402 from Asp85 to Asp212 is correlated with the proton transfer from the Schiff base to Asp85. The interaction of Thr89 and Asp85 is from our FTIR results [11,28]. The orientation of the N – D group in K is from the theoretical calculation [21], which is consistent with our FTIR results [12]. On the other hand, the orientation of the N – D group in L is arbitrary. This figure is modified from Ref. [15].
[10]. These FTIR results are consistent with the structural [16,17] and theoretical [18] studies for the K intermediate. The water band of BR at 2171 cm 1 is changed in K, whereas the band is restored in L, M, and N (Fig. 3). Since the frequency (2171 cm 1) is extremely low for a water stretch, we postulate that the hydrogen-bonding acceptor of the water is negatively charged as is for BR. This means that it would be either Asp85 or Asp212 in L, and Asp212 in M. We proposed that water402 forms strong hydrogen bond (i) with Asp85 in L, and (ii) with Asp212 in M (Fig. 5). The Kto-L transition accompanies relaxation around the retinal chromophore, which involves water structural changes. Reassociation of water402 to Asp85 is one of these changes,
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which presumably stabilizes the negative charge at position 85 in L. According to our model, then, the hydration switch of water402 takes place from Asp85 to Asp212, so that the M intermediate is formed accompanying proton transfer from the Schiff base to Asp85 (Fig. 5). Thus, the simple hydration switch model can explain the present IR data and mechanism of the proton transfer in the Schiff base [15]. Since structures of photointermediates have been reported, it is of interest to compare the distance of a water with the closer carboxyl oxygen in Asp85 or Asp212. According to the L structure by Royant et al. [19], the ˚, distance from water to Asp85 or Asp212 is 2.6 or 2.9 A respectively. The L structure by Lanyi and Schobert [20] shows that the distance from water402 to Asp85 or Asp212 ˚ , respectively. These observations imply that is 2.4 or 3.2 A the water associates stronger with Asp85 than with Asp212, as well as in BR (Figs. 2 and 5). The L structure by Kouyama et al. [21] lacks the water corresponding to water402, because it moves to the cytoplasmic side. In this case, another water molecule hydrating Asp85 may be the candidate of the O –D stretch at 2171 cm 1. On the other hand, ˚ various M structures provided the following values; 3.3 A ˚ with Asp85 and 3.0 A with Asp212 by Luecke et al. for ˚ with Asp85 and 2.9 A ˚ with Asp212 by D96N [22], 2.8 A ˚ ˚ Luecke et al. for E204Q [23], 2.8 A with Asp85 and 2.5 A ˚ with Asp212 by Sass et al. for the wild type [24], 3.1 A with ˚ with Asp212 by Facciotti et al. for the wild Asp85 and 3.0 A ˚ with Asp85 and 2.5 A ˚ with Asp212 by type [25], and 2.4 A Lanyi and Schobert for the wild type [26]. Since the positions of hydrogen atoms are uncertain for these water molecules, it is difficult to conclude the strength of hydrogen bonds quantitatively from these structures. However, the interaction of Asp212 with the water seems to become stronger in M than in L. Hydration switch is a model that motion of a water molecule controls the relative pKa of proton donor and acceptor. Such motion of the water is governed by protein structural changes during the L – M transition. It is noted that the hydration switch model itself does not explain the vectoriality of the proton transport. Rather, they would be in an equilibrium, during which the accessibility of the Schiff base turns to the cytoplasmic side. In the hydration switch model, Asp212 plays an important role in the proton transfer reaction from the Schiff base to Asp85. As compared with Asp85, role of Asp212 has been less understood. Asp212 is a weaker counterion of the protonated Schiff base than Asp85. D212N does not pump protons at >pH 7, even though there are a proton donor (the Schiff base) and an acceptor (Asp85). A negative charge at position 212 seems to work for the dynamics of the primary proton transfer. Accompanying the M-to-N transition, a proton is transferred from Asp96 in the cytoplasmic side to the Schiff base (Fig. 1). The distance between Asp96 and the Schiff base is ˚ in M, and internal water molecules must assist the >11 A proton transfer. In fact, recent crystallographic structure of the N intermediate of the V49A mutant showed the presence
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of a continuous single file of four hydrogen-bonded water molecules [27]. Interestingly, the N minus BR spectrum lacks water vibrations under strong hydrogen-bonding conditions (Fig. 3d), although Asp96 possesses a negative charge. This suggests that there is no strong association of water molecules with the negatively charged Asp96 in N, unlike the case for Asp85 in BR (Fig. 1). Crystal structure suggests the important role of Thr46 in stabilizing the deprotonation state of Asp96 [27]. Spectral acquisition for the X –D stretches also provides information on hydrogen bonds other than water molecules. While the N – D stretch of the Schiff base is at 2171 and 2123 cm 1 for BR and about 2466 cm 1 for K (Fig. 3a, underlined) [12], similar negative bands are observed in the other spectra (Fig. 3b – d). By use of 18O-Thr-labeled BR, we assigned the O – D stretch of Thr89 at 2506 cm 1 for BR, and about 2466 cm 1 for K, L, and M intermediates (Fig. 3a– c) [11,28], leading to a tight, persistent complex between Thr89 and Asp85. Further analysis by use of isotope-labeled BR will lead to better understanding of the hydrogen-bonding alterations during the proton pump in BR.
3. Conclusion and perspectives The experimental observation of internal water molecules by FTIR spectroscopy has allowed to examine their roles in proton pumping by BR. It was revealed that some of internal water molecules form strong hydrogen bond with negative charges in the active center of BR. Proton pump activity seems to be correlated with the presence of internal water molecules under strongly hydrogen-bonded conditions. During the pump process, such strong hydrogen bonds of internal water molecules are rearranged, which plays an essential role in the proton transfer from the Schiff base to Asp85. Role of internal water molecules for other rhodopsins is interesting. Association of water molecules with the negative charges has been commonly found in pharaonis phoborhodopsin ( ppR), where the frequencies at 2307 and 2215 cm 1 indicate weaker hydrogen bonds of internal water molecules in ppR than in BR [29]. Hydration of internal water molecules to a chloride ion in halorhodopsin, a lightdriven chloride pump, is another interest, because crystallographic structure of halorhodopsin showed the presence of the BR-like pentagonal cluster that replaces Asp85 in Fig. 2 by the chloride ion [30]. Role of internal water molecules in chloride pump is in progress by means of low-temperature FTIR spectroscopy. In contrast, there are no spectral changes of water molecules under strongly hydrogen-bonding conditions during the photoactivation processes of bovine rhodopsin, implying that an ion-pair state between the protonated Schiff base and Glu113 in vertebrate visual rhodopsins is stabilized in a manner different from that in archaeal rhodopsins [31]. Further experimental and theoret-
ical efforts will lead to better understanding of the role of internal water molecules in rhodopsins. Acknowledgements I thank Dr. Yuji Furutani, Taro Tanimoto, and Mikihiro Shibata for providing data and discussion. Some of the research described herein was supported by grants from the Japanese Ministry of Education, Culture, Sports, Science, and Technology (14380316, 15076202). References [1] H. Kandori, Role of internal water molecules in bacteriorhodopsin, Biochim. Biophys. Acta 1460 (2000) 177 – 191. [2] J.K. Lanyi, Understanding structure and function in the light-driven proton pump bacteriorhodopsin, J. Struct. Biol. 124 (1998) 164 – 178. [3] U. Haupts, J. Tittor, D. Oesterhelt, Closing in on bacteriorhodopsin: progress in understanding the molecule, Annu. Rev. Biophys. Biomol. Struct. 28 (1999) 367 – 399. [4] M.P. Krebs, H.G. Khorana, Mechanism of light-dependent proton translocation by bacteriorhodopsin, J. Bacteriol. 175 (1993) 1555 – 1560. [5] J. Sasaki, L.S. Brown, Y.-S. Chon, H. Kandori, A. Maeda, R. Needleman, J.K. Lanyi, Conversion of bacteriorhodopsin into a chloride ion pump, Science 269 (1995) 73 – 75. [6] H. Luecke, B. Schobert, H.-T. Richter, J.P. Cartailler, J.K. Lanyi, ˚ resolution, J. Mol. Biol. Structure of bacteriorhodopsin at 1.55 A 291 (1999) 899 – 911. [7] H. Belrhali, P. Nollert, A. Royant, C. Menzel, J. Rosenbusch, E.M. Landau, E. Pebay-Peyroula, Protein, lipid, and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane ˚ resolution, Structure 7 (1999) 909 – 917. at 1.9 A [8] H. Luecke, Atomic resolution structures of bacteriorhodopsin photocycle intermediates: the role of discrete water molecules in the function of this light-driven ion pump, Biochim. Biophys. Acta 1460 (2000) 133 – 156. [9] H. Kandori, N. Kinoshita, Y. Shichida, A. Maeda, Protein structural changes in bacteriorhodopsin upon photoisomerization as revealed by polarized FTIR spectroscopy, J. Phys. Chem., B 102 (1998) 7899 – 7905. [10] H. Kandori, Y. Shichida, Direct observation of the bridged water stretching vibrations inside a protein, J. Am. Chem. Soc. 122 (2000) 11745 – 11746. [11] H. Kandori, N. Kinoshita, Y. Yamazaki, A. Maeda, Y. Shichida, R. Needleman, J.K. Lanyi, M. Bizounok, J. Herzfeld, J. Raap, J. Lugtenburg, Structural change of threonine 89 upon photoisomerization in bacteriorhodopsin as revealed by polarized FTIR spectroscopy, Biochemistry 38 (1999) 9676 – 9683. [12] H. Kandori, M. Belenky, J. Herzfeld, Vibrational frequency and dipolar orientation of the protonated Schiff base in bacteriorhodopsin before and after photoisomerization, Biochemistry 41 (2002) 6026 – 6031. [13] S. Hayashi, I. Ohmine, Proton transfer in bacteriorhodopsin: structure, excitation, IR spectra, and potential energy surface analyses by an ab initio QM/MM method, J. Phys. Chem., B 104 (2000) 10678 – 10691. [14] M. Shibata, T. Tanimoto, H. Kandori, Water molecules in the Schiff base region of bacteriorhodopsin, J. Am. Chem. Soc. 125 (2003) 13312 – 13313. [15] T. Tanimoto, Y. Furutani, H. Kandori, Structural changes of water in the Schiff base region of bacteriorhodopsin: proposal of a hydration switch model, Biochemistry 42 (2003) 2300 – 2306.
H. Kandori / Biochimica et Biophysica Acta 1658 (2004) 72–79 [16] B. Schobert, J. Cupp-Vickery, V. Hornak, S.O. Smith, J.K. Lanyi, Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal, J. Mol. Biol. 321 (2002) 715 – 726. [17] Y. Matsui, K. Sakai, M. Murakami, Y. Shiro, S. Adachi, H. Okumura, T. Kouyama, Specific damage induced by X-ray radiation and structural changes in the primary photoreaction of bacteriorhodopsin, J. Mol. Biol. 324 (2003) 469 – 481. [18] S. Hayashi, E. Tajkhorshid, K. Schulten, Molecular dynamics simulation of bacteriorhodopsin’s photoisomerization using ab initio forces for the excited chromophore, Biophys. J. 83 (2003) 1281 – 1297. [19] A. Royant, K. Edman, T. Ursby, E. Pebay-Peyroula, E.M. Landau, R. Neutze, Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin, Nature 406 (2000) 645 – 648. [20] J.K. Lanyi, B. Schobert, Mechanism of proton transport in bacteriorhodopsin from crystallographic structures of the K, L, M1, M2, and M2V intermediates of the photocycle, J. Mol. Biol. 328 (2003) 439 – 450. [21] T. Kouyama, T. Nishikawa, T. Tokuhisa, H. Okumura, Crystal structure of the L intermediate of bacteriorhodopsin: evidence for vectorial translocation of a water molecule during the proton pumping cycle, J. Mol. Biol. 335 (2004) 531 – 546. [22] H. Luecke, B. Schobert, H.-T. Richter, J.P. Cartailler, J.K. Lanyi, ˚ Structural changes in bacteriorhodopsin during ion transport at 2 A resolution, Science 286 (1999) 255 – 261. [23] H. Luecke, B. Schobert, J.-P. Cartailler, H.-T. Richter, A. Rosengarth, R. Needleman, J.K. Lanyi, Coupling photoisomerization of the retinal in bacteriorhodopsin to directional transport, J. Mol. Biol. 300 (2000) 1237 – 1255. [24] H.J. Sass, G. Bu¨ldt, R. Gessenich, D. Hehn, D. Neff, R. Schlesinger, J. Berendzen, P. Ormos, Structural alterations for proton translocation in the M state of wild-type bacteriorhodopsin, Nature 406 (2000) 649 – 653. [25] M.T. Facciotti, S. Rouhani, F.T. Burkard, F.M. Betancourt, K.H. Downing, R.B. Rose, G. McDermott, R.M. Glaeser, Structure of an
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early intermediate in the M state phase of the bacteriorhodopsin photocycle, Biophys. J. 81 (2002) 3442 – 3455. J.K. Lanyi, B. Schobert, Crystallographic structure of the retinal and the protein after deprotonation of the Schiff base: the switch in the bacteriorhodopsin photocycle, J. Mol. Biol. 321 (2002) 727 – 737. B. Schobert, L.S. Brown, J.K. Lanyi, Crystallographic structures of the M and N intermediates of bacteriorhodopsin: assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff base, J. Mol. Biol. 330 (2003) 553 – 570. H. Kandori, Y. Yamazaki, Y. Shichida, J. Raap, J. Lugtenburg, M. Belenky, J. Lugtenburg, J. Herzfeld, Tight Asp85 – Thr89 association during the pump switch of bacteriorhodopsin, Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 1571 – 1576. Y. Furutani, H. Kandori, Internal water molecules of archaeal rhodopsins, Mol. Membr. Biol. 19 (2002) 257 – 265. M. Kolbe, H. Besir, L.-O. Essen, D. Oesterhelt, Structure of the light˚ resolution, Science 288 driven chloride pump halorhodopsin at 1.8 A (2000) 1390 – 1396. Y. Furutani, Y. Shichida, H. Kandori, Structural changes of water molecules during the photoactivation processes in bovine rhodopsin, Biochemistry 42 (2003) 9619 – 9625. A. Maeda, J. Sasaki, Y. Shichida, T. Yoshizawa, Water structural changes in the bacteriorhodopsin photocycle: analysis by Fourier transform infrared spectroscopy, Biochemistry 31 (1992) 462 – 467. P. Hildebrandt, M. Stockburger, Role of water in bacteriorhodopsin’s chromophore: resonance Raman study, Biochemistry 23 (1984) 5539 – 5548. H.J.M. De Groot, G.S. Harbison, J. Herzfeld, R.G. Griffin, Nuclear magnetic resonance study of the Schiff base in bacteriorhodopsin: counterion effects on the 15N shift anisotropy, Biochemistry 28 (1989) 3346 – 3353. G. Papadopoulos, N.A. Dencher, G. Zaccai, G. Bu¨ldt, Water molecules and exchangeable hydrogen ions at the active center of bacteriorhodopsin localized by neutron diffraction, J. Mol. Biol. 214 (1990) 15 – 19.
Review
Hydration switch model for the proton transfer in the Schiff base region of bacteriorhodopsin Hideki Kandori * Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan Received 18 February 2004; received in revised form 15 March 2004; accepted 15 March 2004 Available online 15 June 2004
Abstract In a light-driven proton-pump protein, bacteriorhodopsin (BR), protonated Schiff base of the retinal chromophore and Asp85 form ionpair state, which is stabilized by a bridged water molecule. After light absorption, all-trans to 13-cis photoisomerization takes place, followed by the primary proton transfer from the Schiff base to Asp85 that triggers sequential proton transfer reactions for the pump. Fourier transform infrared (FTIR) spectroscopy first observed O – H stretching vibrations of water during the photocycle of BR, and accurate spectral acquisition has extended the water stretching frequencies into the entire stretching frequency region in D2O. This enabled to capture the water molecules hydrating with negative charges, and we have identified the water O – D stretch at 2171 cm 1 as the bridged water interacting with Asp85. We found that retinal isomerization weakens the hydrogen bond in the K intermediate, but not in the later intermediates such as L, M, and N. On the basis of the observation particularly on the M intermediate, we proposed a model for the mechanism of proton transfer from the Schiff base to Asp85. In the ‘‘hydration switch model’’, hydration of a water molecule is switched in the M intermediate from Asp85 to Asp212. This will have raised the pKa of the proton acceptor, and the proton transfer is from the Schiff base to Asp85. D 2004 Elsevier B.V. All rights reserved. Keywords: Proton pump; Retinal; Hydrogen bond; Fourier transform infrared spectroscopy; Internal water molecule; Isotope effect
1. Introduction Proteins that actively pump protons across membranes must translocate them through hydrophobic regions inside the protein. Therefore, internal water molecules are presumed to play a crucial role in active proton transport [1]. The water must participate in hydrogen-bonding networks inside proteins that constitute proton pathways. Nevertheless, the proton pathways cannot be fully connected between the two sides of the membrane, because the proton gradient formed will be collapsed. This is an important aspect in distinguishing pumps from channels. The former needs a ‘switch’, which ensures the vectoriality of the pumping. Besides participating in hydrogen-bonding networks, water molecules may be elements of the switch, which mediates an essential proton transfer at the active site. While little is known about the structure and function of internal water
* Fax: +81-52-735-5207. E-mail address: [email protected] (H. Kandori). 0005-2728/$ - see front matter D 2004 Elsevier B.V. All rights reserved. doi:10.1016/j.bbabio.2004.03.015
molecules in such proteins generally, the greatest progress has been made in bacteriorhodopsin (BR). BR is a light-driven proton pump in Halobacterium salinarum that contains all-trans retinal as chromophore (Fig. 1) [2,3]. The retinal binds covalently to Lys216 through a protonated Schiff base. Upon light absorption, photoisomerization takes place from the all-trans to 13-cis form in subpicoseconds, followed by a cyclic reaction that comprises a series of intermediates, designated as the J, K, L, M, N, and O states. Proton pump in BR is achieved by five proton transfer reactions shown in Fig. 1. The primary proton transfer from the Schiff base to Asp85 (1) and the proton release from the groups containing Glu204 and Glu194 (2) occur in the L – M transition of the BR photocycle at neutral pH. The M– N transition accompanies a proton transfer from Asp96 to the Schiff base (3), while the proton uptake occurs in the N –O transition (4). Finally, the proton transfer from Asp85 to the extracellular proton release group takes place in the O – BR transition (5). Although proton transfer reactions inside protein are spatially and temporally well controlled, mutation studies
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and at Arg82, and counterbalancing negative charges located at Asp85 and Asp212 (Fig. 2) [6,7]. The quadrupole inside protein is stabilized by three water molecules (water401, 402, and 406), which constitute a roughly planar pentagonal cluster together with one oxygen each of Asp85 and Asp212. A notable structural feature is that Asp85 and Asp212 are located at similar distances from the retinal Schiff base, whereas the Schiff base proton is transferred only to Asp85 (Fig. 2). The mechanism of the proton transfer from the Schiff base to Asp85 has therefore attracted much interest, and the water molecules in the Schiff base region presumably play important roles in the proton transfer reaction [1]. The Schiff base proton may be transferred through the proton wire formed between the donor (Schiff base) and acceptor (Asp85). On the other hand, it may directly jump between them. Another interesting hypothesis is that ‘‘proton transfer’’ is in fact hydroxide transfer, where a hydroxide (OH ) moves from the extracellular to the cytoplasmic domain as does for a chloride ion in the D85T mutant BR [8]. In any models, important are the intermediate structures before and after the proton transfer (the L and M intermediates, respectively). However, there are variations
Fig. 1. X-ray crystallographic structures of the Schiff base region in BR (PDB entry 1C3W) [6]. Proton pathways are viewed from A-helix, which is removed in the figure. Protonatable groups and bound water molecules are highlighted by stick drawing and green spheres, respectively. Numbers with arrows represent the sequence of proton transfer reactions.
have provided important information. The proton pumping activity is retained upon replacement of terminal protonatable groups such as Asp96, Glu204, and Glu194 [4]. Therefore, even though protons are transferred to and from Asp96 and Glu204 and/or Glu194 during the photocycle, these side chains cannot be actively involved in the switch. In contrast, there is no doubt that Asp85 is involved in the switch, because its replacement results in the loss of proton pumping ability [4]. Not only losing the proton pump function, the replacement of aspartate with threonine at position 85 can convert into a chloride pump like halorhodopsin [5]. Thus, the domain containing Asp85 and the retinal Schiff base is likely to constitute the switch, the heart of the pump. It is generally accepted that the primary proton transfer ensures the directionality in pump, because the accessibility is switched from the extracellular side to the cytoplasmic side, either upon the formation of M or the early-to-late M transition [2,3]. In the Schiff base region, there is a quadrupolar structure with positive charges located at the protonated Schiff base
Fig. 2. X-ray crystallographic structures of the Schiff base region in BR (PDB entry 1C3W) [6]. The membrane normal is approximately in the vertical direction of this figure. Upper and lower regions correspond to the cytoplasmic and extracellular sides, respectively. Green spheres (401, 402, and 406) represent water molecules which form a roughly pentagonal cluster with an oxygen from Asp85 and an oxygen from Asp212. Watercontaining pentagonal cluster structure will stabilize an electric quadrupole in this region. Hydrogen atoms and hydrogen bonds (dotted lines) are supposed from the structure, while the numbers are the hydrogen-bonding ˚ . After photoisomerization of the retinal, the Schiff base distances in A proton is transferred to Asp85 in the L-to-M transition (arrow), although two aspartates are located symmetrically.
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among the reported crystallographic structures of photointermediates. It should be emphasized that tiny difference in bond angle in retinal could lead to significant difference in the orientation of the N-H group of the Schiff base. Similar argument is possible for the positions of internal water molecules. A different approach to internal water molecules of BR is shown in this review article. Here I introduce our recent studies on the internal water molecules by means of Fourier transform infrared (FTIR) spectroscopy.1 Detection of internal water molecules under strong hydrogen bonds is one of recent highlights, and a model for the primary proton transfer reaction is proposed on the basis of such measurements.
2. FTIR studies of internal water molecules of BR 2.1. Detection of water in the primary reaction of BR FTIR spectroscopy of biological molecules is usually applied in the frequency region < 1800 cm 1, giving secondary structural information. Strong absorption of water molecules in the 3700 –3000 cm 1 region prevents from obtaining accurate spectra in the region. That is, information of internal water molecules is easily masked by solvent water molecules, as the latter are much more numerous. However, it is known that BR films exhibit a normal photocycle under suitable hydration conditions. In addition, BR being a photoreceptive protein, the protein conformation changes are conveniently obtained as difference IR spectra. These facts allowed to obtain difference IR spectra in the frequency region not only < 1800 cm 1, but also in the water stretching region. This author reviewed the details of the historical aspects of FTIR studies on BR in this journal 4 years ago [1]. O –H stretching vibrations of water molecules were identified by comparing hydrations of H2O and H218O. Then, various mutants have been tested for several intermediate states, which provided information on the location of bound water molecules to BR. As described in the review, however, there was a limitation in frequency for the previous FTIR measurements, where the observed frequency region of water molecules in the previous FTIR studies was limited in the >3450 cm 1 [1]. It is noted that the O – H stretching frequency is lowered when hydrogen bond is strengthened. This means that FTIR spectroscopy has been able to detect only the narrow region for rather free O – H groups, while information on the bridged water O – H through hydrogen bonding was not possible to obtain. The Schiff base structure in Fig. 2 suggests the importance to probe water 1
History of the study on internal water molecules of BR was reviewed in detail in the previous article [1]. The first FTIR study on water molecules was reported in 1992 by Maeda et al. [32]. Before the report, internal water molecules of BR were also discussed on the basis of resonance Raman spectroscopy [33], NMR spectroscopy [34], and neutron diffraction [35].
vibrations under strong hydrogen bonds. The reason for the difficulty in identifying water O –H bands in the lower frequency region is as follows: (i) the spectral accuracy is less because of intense absorption by water, (ii) many protein bands other than water O – H stretches overlap this region, and (iii) strongly hydrogen-bonded water possesses broad O –H stretching bands. These facts have disturbed observations of clear isotope shifts. In particular, an isotope shift between O – H and 18O – H is about 10 cm 1, and such small shift could be hidden in complex spectral features in the 3450 –3000-cm 1 region. About 6 years ago, we attempted to extend the frequency region of water stretching vibrations that monitor strong hydrogen bonds. By optimizing the measuring system of polarized FTIR spectroscopy, we could measure the K minus BR difference spectra in whole mid-infrared region (4000 – 700 cm 1) [9]. One of the key issues was to obtain the difference spectra in D2O, by which the D2O-insensitive stretching vibrations are separated in frequency. On the other hand, BR pumps deuterium in D2O, so that the O – H groups of internal water molecules that participate proton transport should be exchanged for O –D groups. We thus expected to observe the isotope shift even for the bridged water stretches. The K minus BR difference spectra in Fig. 3a indeed show the isotope shift of water not only for weak hydrogen bonds (2700 – 2500 cm 1), but also for strong hydrogen bonds ( < 2400 cm 1) [10]. There are at least six negative bands of water O –D stretches at 2690, 2636, 2599, 2323, 2292, and 2171 cm 1, indicating that retinal photoisomerization alters hydrogen bonds of several water molecules. Interestingly, the observed water bands were at 2700– 2600 and 2350 –2150 cm 1, locating at both edges in broad absorption spectra of D2O (gray spectra in Fig. 3). This fact suggests that these water molecules are specifically bound to protein. It is particularly noted that the O –D stretch at 2171 cm 1 is much lower in frequency than those for the fully hydrated tetrahedral water molecules, suggesting that the hydrogen bond acceptor of this water molecule is negatively charged, such as oxygens of Asp85 and Asp212 (Fig. 2) [10]. Fig. 3a shows that most bands in the 2700 – 2000 cm 1 region originate from water O – D stretches. On the other hand, some other bands have been already identified. We assigned the 2506 ( )/2466 (+) cm 1 bands as the O –D stretch of Thr89 by use of [3-18O]threonine-labeled BR sample [11]. Low frequency (2506 cm 1) as the threonine O – D stretch in BR indicates strong hydrogen bond of Thr89, which is consistent with the BR structure (Fig. 2). Lower frequency shift to 2466 cm 1 in K implies further strengthened hydrogen bond of Thr89 presumably with Asp85. We assigned the negative 2171 and 2123 cm 1 bands contain N –D stretch of the Schiff base by use of [s-15N]lysine-labeled BR sample [12]. The presence of the N –D stretch of the Schiff base at the same frequency as the O –D stretch of water is one of the reasons of small isotope
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1 Fig. 3. Difference IR spectra are compared between hydration with D2O (red lines) and D18 region. The window tilting 2 O (blue lines) in the 2750 – 1930 cm angles are 53.5j in the polarized IR measurements. The K minus BR (a), L minus BR (b), M minus BR (c) and N minus BR (d) spectra are measured at 77, 170, 230, and 273 K, respectively. The gray curve in the 2700 – 2000 cm 1 region represents O – D stretching vibrations of D2O. Green-labeled frequencies correspond to those identified as water stretching vibrations. Purple-labeled frequencies are O – D stretch of Thr89 [11,28], while the underlined-frequencies are N – D stretch of the Schiff base [12]. This figure is modified from Ref. [15].
shift of water for the 2171 cm 1 band (Fig. 3a). The ND stretch of the Schiff base appears at about 2466 cm 1 in the K intermediate, indicating that the hydrogen bond of the Schiff base is significantly weakened. Polarized measurements suggested that the N –D group of the Schiff base in K orients along the membrane [12]. Thus, Fig. 3a exhibits strong perturbation of the Schiff base region (Fig. 1) upon retinal photoisomerization through the analysis of stretching vibrations. 2.2. Assignment of the O –D stretch at 2171 cm
1
in BR
Since vibrational bands of water molecules are obtained, normal mode analysis is important on the basis of the BR structure (Fig. 2). In the same year of our IR study, Hayashi and Ohmine [13] reported the quantum mechanical and molecular mechanical (QM/MM) calculation of the Schiff base region in BR. According to their calculation, the water O – D stretch at the lowest frequency (2171 cm 1) corresponds to the stretching mode of water402 bound to Asp85, while another O – D stretch of water402 is about 350 cm 1 higher in frequency. This means that the hydrogen bond of water402 with Asp85 is much stronger than that with Asp212, even though it is not clear from Fig. 2. Stronger association with Asp85 may be related to the fact that Asp85 is the principal counterion of the protonated Schiff base. However, it should be noted that the 2171 cm 1 band has not been experimentally proven to be the O –D stretch of water402 interacting with Asp85. Therefore, we next measured the K minus BR spectra for various BR mutants [14].
If the 2171 cm 1 band originates from the O –D stretch of water402 hydrating Asp85, as predicted by Hayashi and Ohmine, removal of the negative charge at the position 85 by a mutation should significantly affect the band. Fig. 4b indeed shows that the broad negative feature in the 2300– 2000 cm 1 region does not exhibit the isotope shift in D85N. The negative band can be assigned as the N –D stretch of the Schiff base like in the wild type BR [12]. D85N lacks not only the 2171 cm 1 band, but also all water bands in this frequency region, suggesting the important role of the negative charge at the position 85. We also expected that the lack of the negative charge at the position 212 will not significantly affect the 2171 cm 1 band according to Hayashi and Ohmine. Nevertheless, Fig. 4c shows that all water bands disappear in the < 2400 cm 1 region in D212N. The results of both D85N and D212N imply the crucial role of each negative charge in the pentagonal cluster, leading to the possible assignment of the water bands at 2323, 2292, and 2171 cm 1 as the O –D stretches involved in the pentagonal cluster (Fig. 2). On the other hand, we could not establish that the 2171 cm 1 band originates from the O – D stretch of water402 hydrating Asp85. It seems that Asp85 and Asp212 are directly involved in the pentagonal cluster structure, so that their mutations greatly change the hydrogen bonding structure. Subsequently, we performed additional mutation studies. One oxygen atom of Asp85 and Asp212 is involved in the pentagonal cluster, while another oxygen forms a hydrogen bond with Thr89 and Tyr185, respectively (Fig. 2). Therefore, we expected that the cleavage of these hydrogen bonds
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molecules suggests that the hydrogen bonding interaction of water402 is stronger with Asp85 than with Asp212 [14]. Since the bridged water interacts more strongly with Asp85, Asp85 is presumably a stronger counterion than Asp212. The role of the negative charge on Asp212 is also crucial. If it is neutralized, all the bands of strongly hydrogen-bonded water molecules disappear (Fig. 2c). Thus, the pentagonal cluster structure composed of the two negative charges may be essential for the function of BR. In fact, D85N and D212N proteins do not pump protons, while mutants of Tyr185 and Thr89 do [4]. Measurements of various mutant proteins are in progress to test the hypothesis that ‘proton pump activity is correlated with the presence of internal water molecules under strongly hydrogen-bonded conditions’. 2.3. Hydration switch model
Fig. 4. The K minus BR difference infrared spectra of the wild type (a), D85N (b), D212N (c), Y185F (d), and T89A (e) BR in the 2380 – 2000 cm 1 region. The samples were hydrated with D2O (red lines) or D18 2 O (blue lines), and spectra were measured at 77 K. Labeled frequencies correspond to these bands identified as water stretching vibrations. This figure is modified from Ref. [14].
would localize the negative charges onto the respective oxygens of the pentagonal cluster. As a consequence, the 2171 cm 1 band would be further down-shifted in a mutant of Thr89, while it would not be much influenced in a mutant of Tyr185. That was indeed the case. Fig. 2d shows that the 2171 cm 1 band of water is preserved in the Y185F mutant, as well as the two positive and the two negative bands of water. On the other hand, a strong negative band appears at 2088 cm 1 in the T89A mutant, which exhibits lower frequency shift in D218O. The frequency change by >80 cm 1 in T89A, but not in Y185F, strongly supports the proposal by the QM/MM calculation that the 2171 cm 1 band originates from the O – D stretch of water402 [13]. The negative peak is present at 2166 and 2155 cm 1 in T89S and T89C, respectively, implying that the hydrogen-bonding interactions with Thr89 and water402 determine negative charge distribution between the side chain oxygens of Asp85 [14]. According to the X-ray structure of BR, Asp85 and Asp212 look symmetrical in the pentagonal cluster structure (Fig. 1). However, the FTIR study of internal water
Since the IR observations of the O – D stretch of water in their entire stretching vibrational frequencies provided new information on the water structural changes before and after retinal isomerization [10], their extension study for late photointermediates will lead to better understanding of water structural changes during proton pump of BR. Therefore, we measured the IR difference spectra in the water O – D stretching region of the L, M, and N intermediates. Fig. 3 shows that no isotope effect of water was observed in the < 2500 cm 1 region for the L minus BR (b), M minus BR (c), and N minus BR (d) spectra, being in clear contrast to the K minus BR (a) spectra [15]. Water stretching vibrations were only observed at >2500 cm 1. The negative band at 2690 cm 1 was commonly observed among all spectra, and the previous mutation studies for the O – H stretching region revealed that the location of the water molecule is near Asp85 [1]. The L minus BR spectrum exhibits the additional negative water band at 2669 cm 1, while broad positive feature due to water appeared in the 2650– 2560 cm 1 region (Fig. 3b), whose locations were estimated to be at the cytoplasmic region [1]. The M minus BR spectrum exhibits the positive water bands at 2715 and 2640 cm 1, whose locations were suggested to be at the cytoplasmic region [1]. Unlike in K, we did not observe spectral changes of the water bands under strong hydrogen-bonding conditions in L, M, and N (Fig. 3). It is particularly noted that the 2171 cm 1 band as the O – D stretch of water402 hydrating with Asp85 was not observed for the L minus BR and M minus BR spectra. On the basis of these IR observations, we interpreted the proton transfer mechanism from the Schiff base to Asp85 as follows. In BR, the O – D stretch of water402 bound to Asp85 is at 2171 cm 1 (Fig. 5). Upon photoisomerization, the N – D group of the Schiff base displaces to form parallel orientation to the membrane [12]. As a consequence, the water-containing pentagonal cluster structure is perturbed, and the interaction between water402 and Asp85 is weakened (Fig. 5). Such structural change possibly involves rotational motion of water402
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Fig. 5. Hydration switch model as the proton transfer mechanism from the Schiff base to Asp85. Structure of the Schiff base region in D2O is schematically drawn. Strong hydrogen bond of water402, whose O – D stretch appears at 2171 cm 1, is highlighted in BR, L, and M. The acceptor is Asp85 in BR and L, while being switched to Asp212 in M. In this model, hydration switch of water402 from Asp85 to Asp212 is correlated with the proton transfer from the Schiff base to Asp85. The interaction of Thr89 and Asp85 is from our FTIR results [11,28]. The orientation of the N – D group in K is from the theoretical calculation [21], which is consistent with our FTIR results [12]. On the other hand, the orientation of the N – D group in L is arbitrary. This figure is modified from Ref. [15].
[10]. These FTIR results are consistent with the structural [16,17] and theoretical [18] studies for the K intermediate. The water band of BR at 2171 cm 1 is changed in K, whereas the band is restored in L, M, and N (Fig. 3). Since the frequency (2171 cm 1) is extremely low for a water stretch, we postulate that the hydrogen-bonding acceptor of the water is negatively charged as is for BR. This means that it would be either Asp85 or Asp212 in L, and Asp212 in M. We proposed that water402 forms strong hydrogen bond (i) with Asp85 in L, and (ii) with Asp212 in M (Fig. 5). The Kto-L transition accompanies relaxation around the retinal chromophore, which involves water structural changes. Reassociation of water402 to Asp85 is one of these changes,
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which presumably stabilizes the negative charge at position 85 in L. According to our model, then, the hydration switch of water402 takes place from Asp85 to Asp212, so that the M intermediate is formed accompanying proton transfer from the Schiff base to Asp85 (Fig. 5). Thus, the simple hydration switch model can explain the present IR data and mechanism of the proton transfer in the Schiff base [15]. Since structures of photointermediates have been reported, it is of interest to compare the distance of a water with the closer carboxyl oxygen in Asp85 or Asp212. According to the L structure by Royant et al. [19], the ˚, distance from water to Asp85 or Asp212 is 2.6 or 2.9 A respectively. The L structure by Lanyi and Schobert [20] shows that the distance from water402 to Asp85 or Asp212 ˚ , respectively. These observations imply that is 2.4 or 3.2 A the water associates stronger with Asp85 than with Asp212, as well as in BR (Figs. 2 and 5). The L structure by Kouyama et al. [21] lacks the water corresponding to water402, because it moves to the cytoplasmic side. In this case, another water molecule hydrating Asp85 may be the candidate of the O –D stretch at 2171 cm 1. On the other hand, ˚ various M structures provided the following values; 3.3 A ˚ with Asp85 and 3.0 A with Asp212 by Luecke et al. for ˚ with Asp85 and 2.9 A ˚ with Asp212 by D96N [22], 2.8 A ˚ ˚ Luecke et al. for E204Q [23], 2.8 A with Asp85 and 2.5 A ˚ with Asp212 by Sass et al. for the wild type [24], 3.1 A with ˚ with Asp212 by Facciotti et al. for the wild Asp85 and 3.0 A ˚ with Asp85 and 2.5 A ˚ with Asp212 by type [25], and 2.4 A Lanyi and Schobert for the wild type [26]. Since the positions of hydrogen atoms are uncertain for these water molecules, it is difficult to conclude the strength of hydrogen bonds quantitatively from these structures. However, the interaction of Asp212 with the water seems to become stronger in M than in L. Hydration switch is a model that motion of a water molecule controls the relative pKa of proton donor and acceptor. Such motion of the water is governed by protein structural changes during the L – M transition. It is noted that the hydration switch model itself does not explain the vectoriality of the proton transport. Rather, they would be in an equilibrium, during which the accessibility of the Schiff base turns to the cytoplasmic side. In the hydration switch model, Asp212 plays an important role in the proton transfer reaction from the Schiff base to Asp85. As compared with Asp85, role of Asp212 has been less understood. Asp212 is a weaker counterion of the protonated Schiff base than Asp85. D212N does not pump protons at >pH 7, even though there are a proton donor (the Schiff base) and an acceptor (Asp85). A negative charge at position 212 seems to work for the dynamics of the primary proton transfer. Accompanying the M-to-N transition, a proton is transferred from Asp96 in the cytoplasmic side to the Schiff base (Fig. 1). The distance between Asp96 and the Schiff base is ˚ in M, and internal water molecules must assist the >11 A proton transfer. In fact, recent crystallographic structure of the N intermediate of the V49A mutant showed the presence
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of a continuous single file of four hydrogen-bonded water molecules [27]. Interestingly, the N minus BR spectrum lacks water vibrations under strong hydrogen-bonding conditions (Fig. 3d), although Asp96 possesses a negative charge. This suggests that there is no strong association of water molecules with the negatively charged Asp96 in N, unlike the case for Asp85 in BR (Fig. 1). Crystal structure suggests the important role of Thr46 in stabilizing the deprotonation state of Asp96 [27]. Spectral acquisition for the X –D stretches also provides information on hydrogen bonds other than water molecules. While the N – D stretch of the Schiff base is at 2171 and 2123 cm 1 for BR and about 2466 cm 1 for K (Fig. 3a, underlined) [12], similar negative bands are observed in the other spectra (Fig. 3b – d). By use of 18O-Thr-labeled BR, we assigned the O – D stretch of Thr89 at 2506 cm 1 for BR, and about 2466 cm 1 for K, L, and M intermediates (Fig. 3a– c) [11,28], leading to a tight, persistent complex between Thr89 and Asp85. Further analysis by use of isotope-labeled BR will lead to better understanding of the hydrogen-bonding alterations during the proton pump in BR.
3. Conclusion and perspectives The experimental observation of internal water molecules by FTIR spectroscopy has allowed to examine their roles in proton pumping by BR. It was revealed that some of internal water molecules form strong hydrogen bond with negative charges in the active center of BR. Proton pump activity seems to be correlated with the presence of internal water molecules under strongly hydrogen-bonded conditions. During the pump process, such strong hydrogen bonds of internal water molecules are rearranged, which plays an essential role in the proton transfer from the Schiff base to Asp85. Role of internal water molecules for other rhodopsins is interesting. Association of water molecules with the negative charges has been commonly found in pharaonis phoborhodopsin ( ppR), where the frequencies at 2307 and 2215 cm 1 indicate weaker hydrogen bonds of internal water molecules in ppR than in BR [29]. Hydration of internal water molecules to a chloride ion in halorhodopsin, a lightdriven chloride pump, is another interest, because crystallographic structure of halorhodopsin showed the presence of the BR-like pentagonal cluster that replaces Asp85 in Fig. 2 by the chloride ion [30]. Role of internal water molecules in chloride pump is in progress by means of low-temperature FTIR spectroscopy. In contrast, there are no spectral changes of water molecules under strongly hydrogen-bonding conditions during the photoactivation processes of bovine rhodopsin, implying that an ion-pair state between the protonated Schiff base and Glu113 in vertebrate visual rhodopsins is stabilized in a manner different from that in archaeal rhodopsins [31]. Further experimental and theoret-
ical efforts will lead to better understanding of the role of internal water molecules in rhodopsins. Acknowledgements I thank Dr. Yuji Furutani, Taro Tanimoto, and Mikihiro Shibata for providing data and discussion. Some of the research described herein was supported by grants from the Japanese Ministry of Education, Culture, Sports, Science, and Technology (14380316, 15076202). References [1] H. Kandori, Role of internal water molecules in bacteriorhodopsin, Biochim. Biophys. Acta 1460 (2000) 177 – 191. [2] J.K. Lanyi, Understanding structure and function in the light-driven proton pump bacteriorhodopsin, J. Struct. Biol. 124 (1998) 164 – 178. [3] U. Haupts, J. Tittor, D. Oesterhelt, Closing in on bacteriorhodopsin: progress in understanding the molecule, Annu. Rev. Biophys. Biomol. Struct. 28 (1999) 367 – 399. [4] M.P. Krebs, H.G. Khorana, Mechanism of light-dependent proton translocation by bacteriorhodopsin, J. Bacteriol. 175 (1993) 1555 – 1560. [5] J. Sasaki, L.S. Brown, Y.-S. Chon, H. Kandori, A. Maeda, R. Needleman, J.K. Lanyi, Conversion of bacteriorhodopsin into a chloride ion pump, Science 269 (1995) 73 – 75. [6] H. Luecke, B. Schobert, H.-T. Richter, J.P. Cartailler, J.K. Lanyi, ˚ resolution, J. Mol. Biol. Structure of bacteriorhodopsin at 1.55 A 291 (1999) 899 – 911. [7] H. Belrhali, P. Nollert, A. Royant, C. Menzel, J. Rosenbusch, E.M. Landau, E. Pebay-Peyroula, Protein, lipid, and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane ˚ resolution, Structure 7 (1999) 909 – 917. at 1.9 A [8] H. Luecke, Atomic resolution structures of bacteriorhodopsin photocycle intermediates: the role of discrete water molecules in the function of this light-driven ion pump, Biochim. Biophys. Acta 1460 (2000) 133 – 156. [9] H. Kandori, N. Kinoshita, Y. Shichida, A. Maeda, Protein structural changes in bacteriorhodopsin upon photoisomerization as revealed by polarized FTIR spectroscopy, J. Phys. Chem., B 102 (1998) 7899 – 7905. [10] H. Kandori, Y. Shichida, Direct observation of the bridged water stretching vibrations inside a protein, J. Am. Chem. Soc. 122 (2000) 11745 – 11746. [11] H. Kandori, N. Kinoshita, Y. Yamazaki, A. Maeda, Y. Shichida, R. Needleman, J.K. Lanyi, M. Bizounok, J. Herzfeld, J. Raap, J. Lugtenburg, Structural change of threonine 89 upon photoisomerization in bacteriorhodopsin as revealed by polarized FTIR spectroscopy, Biochemistry 38 (1999) 9676 – 9683. [12] H. Kandori, M. Belenky, J. Herzfeld, Vibrational frequency and dipolar orientation of the protonated Schiff base in bacteriorhodopsin before and after photoisomerization, Biochemistry 41 (2002) 6026 – 6031. [13] S. Hayashi, I. Ohmine, Proton transfer in bacteriorhodopsin: structure, excitation, IR spectra, and potential energy surface analyses by an ab initio QM/MM method, J. Phys. Chem., B 104 (2000) 10678 – 10691. [14] M. Shibata, T. Tanimoto, H. Kandori, Water molecules in the Schiff base region of bacteriorhodopsin, J. Am. Chem. Soc. 125 (2003) 13312 – 13313. [15] T. Tanimoto, Y. Furutani, H. Kandori, Structural changes of water in the Schiff base region of bacteriorhodopsin: proposal of a hydration switch model, Biochemistry 42 (2003) 2300 – 2306.
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