FTIR detection of water reactions in the oxygen-evolving centre of photosystem II

Flash-induced Fourier transform infrared (FTIR) difference spectroscopy has been used to study the water-oxidizing reactions in the oxygen-evolving centre of photosystem II. Reactions of water molecules were directly monitored by detecting the OH stretching bands of weakly H-bonded OH of water in the 3700-3500 cm(-1) region in FTIR difference spectra during S-state cycling. In the S1-->S2 transition, a band shift from 3588 to 3617 cm(-1) was observed, indicative of a weakened H-bond. Decoupling experiments using D2O:H2O (1:1) showed that this OH arose from a water molecule with an asymmetric H-bonding structure and this asymmetry became more significant upon S2 formation. In the S2-->S3, S3-->S0 and S0-->S1 transitions, negative bands were observed at 3634, 3621 and 3612 cm(-1), respectively, representing formation of a strong H-bond or a proton release reaction. In addition, using complex spectral features in the carboxylate stretching region (1600-1300 cm-(1)) as 'fingerprints' of individual S-state transitions, pH dependency of the transition efficiencies and the effect of dehydration were examined to obtain the information of proton release and water insertion steps in the S-state cycle. Low-pH inhibition of the S2-->S3, S3-->S0 and S0-->S1 transitions was consistent with a view that protons are released in the three transitions other than S1-->S2, while relatively high susceptibility to dehydration in the S2-->S3 and S3-->S0 transitions suggested the insertion of substrate water into the system during these transitions. Thus, a possible mechanism of water oxidation to explain the FTIR data is proposed.     

FTIR detection of water reactions during the flash-induced S-state cycle of the photosynthetic water-oxidizing complex

Photosynthetic water oxidation is performed via the light-driven S-state cycle in the water-oxidizing complex (WOC) of photosystem II (PS II). To understand its molecular mechanism, monitoring the reaction of substrate water in each S-state transition is essential. We have for the first time detected the reactions of water molecules in WOC throughout the S-state cycle by observing the OH vibrations of water using flash-induced Fourier transform infrared (FTIR) difference spectroscopy. Moderately hydrated (or deuterated) PS II core films from Synechococcus elongatus were used to obtain the FTIR difference spectra upon the first, second, third, and fourth flash illumination, representing the structural changes in the S(1) --> S(2), S(2) --> S(3), S(3) --> S(0), and S(0) --> S(1) transitions, respectively. In the weakly H-bonded OH region, bands appeared at 3617/3588 cm(-1) as a differential signal in the first-flash spectrum and at 3634, 3621, and 3612 cm(-1) with negative intensities in the second-, third-, and fourth-flash spectra, respectively. These bands shifted down by approximately 940 cm(-1) upon deuteration and by approximately 10 cm(-1) upon H(18)O substitution, indicating that they arise from the OH stretches of water including the substrate and its intermediates. Strongly D-bonded OD bands of water were also identified as broad features in the range of 2600-2200 cm(-1) by taking the double difference between the spectra of D(2)(16)O- and D(2)(18)O-deuterated films. In addition, broad continuum features that probably arise from the large proton polarizability of H-bonds were observed around 3000, 2700, 2550, and 2600 cm(-1) in the first-, second-, third-, and fourth-flash spectra, respectively, of the hydrated PS II film, revealing changes in the H-bond network of the protein. The negative OH intensities upon the second to fourth flashes might be related to proton release from substrate water. The results presented here showed that FTIR detection of water OH(D) bands can be a powerful method for investigating the mechanism of photosynthetic water oxidation.     

Monitoring water reactions during the S-state cycle of the photosynthetic water-oxidizing center: detection of the DOD bending vibrations by means of Fourier transform infrared spectroscopy

Photosynthetic water oxidation takes place in the water-oxidizing center (WOC) of photosystem II (PSII). To clarify the mechanism of water oxidation, detecting water molecules in the WOC and monitoring their reactions at the molecular level are essential. In this study, we have for the first time detected the DOD bending vibrations of functional D 2O molecules during the S-state cycle of the WOC by means of Fourier transform infrared (FTIR) difference spectroscopy. Flash-induced FTIR difference spectra upon S-state transitions were measured using the PSII core complexes from Thermosynechococcus elongatus moderately deuterated with D 2 (16)O and D 2 (18)O. D 2 (16)O-minus-D 2 (18)O double difference spectra at individual S-state transitions exhibited six to eight peaks arising from the D (16)OD/D (18)OD bending vibrations in the 1250-1150 cm (-1) region. This observation indicates that at least two water molecules, not in any deprotonated forms, participate in the reaction at each S-state transition throughout the cycle. Most of the peaks exhibited clear counter peaks with opposite signs at different transitions, reflecting a series of reactions of water molecules at the catalytic site. In contrast, negative bands at approximately 1240 cm (-1) in the S 2 --> S 3, S 3 --> S 0, and possibly S 0 --> S 1 transitions, for which no clear counter peaks were found in other transitions, can be interpreted as insertion of substrate water into the WOC from a water cluster in the proteins. The characteristics of the weakly D-bonded OD stretching bands were consistent with the insertion of substrate from internal water molecules in the S 2 --> S 3 and S 3 --> S 0 transitions. The results of this study show that FTIR detection of the DOD bending vibrations is a powerful method for investigating the molecular mechanism of photosynthetic water oxidation as well as other enzymatic reactions involving functional water molecules.     

FTIR spectroscopy of the O photointermediate in pharaonis phoborhodopsin

pharaonis phoborhodopsin (ppR; also called pharaonis sensory rhodopsin II, psR-II) is a photoreceptor protein for negative phototaxis in Natronobacterium pharaonis. During the photocycle of ppR, the retinal chromophore is thermally isomerized from the 13-cis to all-trans form. We employed FTIR spectroscopy of ppR at 260 K and pH 5 to reveal that this isomerization occurs upon formation of the O intermediate (ppR(O)) by using ppR samples reconstituted with 12,14-D(2)-labeled retinal. In ppR(O), C=O stretching vibrations of protonated carboxylates newly appear at 1757 (+)/1722 (-) cm(-1) in H(2)O and at 1747 (+)/1718 (-) cm(-1) in D(2)O in addition to the 1765 (+) cm(-1) band of Asp75. Amide I vibrations are basically similar between ppR(M) and ppR(O), whereas unique bands of ppR(O) are also observed such as the negative 1656 cm(-1) band in D(2)O and intense bands at 1686 (-)/1674 (+) cm(-1). In addition, O-D stretching vibrations of water molecules in the entire mid-infrared region are assigned for ppR(M) and ppR(O), the latter being unique for ppR, since it can be detected at low temperature (260 K). The ppR(M) minus ppR difference spectra lack the lowest frequency water band (2215 cm(-1)) observed in the ppR(K) minus ppR spectra, which is probably associated with water that interacts with the negative charges in the Schiff base region. It is likely that the proton transfer from the Schiff base to Asp75 in ppR(M) can be explained by a hydration switch of a water from Asp75 to Asp201, as was proposed for the light-driven proton-pump bacteriorhodopsin (hydration switch model) [Tanimoto, T., Furutani, Y., and Kandori, H. (2003) Biochemistry 42, 2300-2306]. In the transition from ppR(M) to ppR(O), a hydrogen-bonding alteration takes place for another water molecule that forms a strong hydrogen bond.     

Flash-induced FTIR difference spectra of the water oxidizing complex in moderately hydrated photosystem II core films: effect of hydration extent on S-state transitions

Differently hydrated films of photosystem II (PSII) core complexes from Synechococcus elongatus were prepared in a humidity-controlled infrared cell. The relative humidity was changed by a simple method of placing a different ratio of glycerol/water solution in the sealed cell. The extent of hydration of the PSII film was lowered as the glycerol ratio increased. FTIR difference spectra of the water oxidizing complex upon the first to sixth flashes were measured at 10 degrees C using these hydrated PSII films. The FTIR spectra (1800-1200 cm(-1)) of the PSII films hydrated using 20% and 40% glycerol/water showed basically the same features as those of the core sample in solution [Noguchi, T., and Sugiura, M. (2001) Biochemistry 40, 1497-1502], and the prominent peaks exhibited clear period four oscillation patterns. These observations indicate that the S-state cycle properly functions in these hydrated samples. In the PSII films less hydrated, however, the efficiencies of S-state transitions decreased as the extent of hydration was lowered. This tendency was more significant in the S2 --> S3 and S3 --> S0 transitions than in the S1 --> S2 and S0 --> S1 transitions, indicating that the reactions or movements of water molecules are more strongly coupled with the former two transitions than the latter two. The implication of this observation was discussed in light of the water oxidizing mechanism especially in respect to the steps of substrate incorporation and proton release. Furthermore, in the OH stretching region (3800-3000 cm(-1)) of the first-flash spectrum, a differential signal was observed at 3618/3585 cm(-1), which was previously found in the S2/S1 spectrum of a frozen sample at 250 K and assigned to the water vibrations [Noguchi, T., and Sugiura, M. (2000) Biochemistry 39, 10943-10949]. The fact that the signal appeared even in rather dehydrated PSII films at a physiological temperature (10 degrees C) supported the idea that this water is located in the close vicinity of the Mn cluster and directly involved in the water oxidizing reaction. The results also showed that moderate hydration of the PSII sample made the whole OH region measurable, escaping from absorption saturation by bulk water, and thus will be a useful technique to monitor the water reactions during the S-state cycle using FTIR spectroscopy.     

Water structural changes involved in the activation process of photoactive yellow protein

Fourier transform infrared (FTIR) spectroscopy was applied to the blue-light photoreceptor photoactive yellow protein (PYP) to investigate water structural changes possibly involved in the photocycle of PYP. Photointermediates were stabilized at low temperature, and difference IR spectra were obtained between intermediate states and the original state of PYP (pG). Water structural changes were never observed in the >3570 cm(-)(1) region for the intermediates stabilized at 77-250 K, such as the red-shifted pR and blue-shifted pB intermediates. In contrast, a negative band was observed at 3658 cm(-)(1) in the pB minus pG spectrum at 295 K, which shifts to 3648 cm(-)(1) upon hydration with H(2)(18)O. The high frequency of the O-H stretch of water indicates that the water O-H group does not form hydrogen bonds in pG, and newly forms these upon pB formation at 295 K, but not at 250 K. Among 92 water molecules in the crystal structure of PYP, only 1 water molecule, water-200, is present in a hydrophobic core inside the protein. The amide N-H of Gly-7 and the imidazole nitrogen atom of His-108 are its possible hydrogen-bonding partners, indicating that one O-H group of water-200 is free to form an additional hydrogen bond. The water band at 3658 cm(-)(1) was indeed diminished in the H108F protein, which strongly suggests that the water band originates from water-200. Structural changes of amide bands in pB were much greater in the wild-type protein at 295 K than at 250 K or in the H108F protein at 295 K. The position of water-200 is >15 A remote from the chromophore. Virtually no structural changes were reported for regions larger than a few angstroms away from the chromophore, in the time-resolved X-ray crystallography experiments on pB. On the basis of the present results, as well as other spectroscopic observations, we conclude that water-200 (buried in a hydrophobic core in pG) is exposed to the aqueous phase upon formation of pB in solution. In neither crystalline PYP nor at low temperature is this structural transition observed, presumably because of the restrictions on global structural changes in the protein under these conditions.     

Water-mediated hydrogen-bonded network on the cytoplasmic side of the Schiff base of the L photointermediate of bacteriorhodopsin

The L intermediate in the proton-motive photocycle of bacteriorhodopsin is the starting state for the first proton transfer, from the Schiff base to Asp85, in the formation of the M intermediate. Previous FTIR studies of L have identified unique vibration bands caused by the perturbation of several polar amino acid side chains and several internal water molecules located on the cytoplasmic side of the retinylidene chromophore. In the present FTIR study we describe spectral features of the L intermediate in D(2)O in the frequency region which includes the N-D stretching vibrations of the backbone amides. We show that a broad band in the 2220-2080 cm(-1) region appears in L. By use of appropriate (15)N labeling and mutants, the lower frequency side of this band in L is assigned to the amides of Lys216 and Gly220. These amides are coupled to each other, and interact with Thr46 and Val49 in helix B and Asp96 in helix C via weakly H-bonding water molecules that exhibit O-D stretching vibrations at 2621 and 2605 cm(-1). These water molecules are part of a hydrogen-bonded network characteristic of L which includes other water molecules located closer to the chromophore that exhibit an O-D stretching vibration at 2589 cm(-1). This structure, extending from the Schiff base to the internal proton donor Asp96, stabilizes L and affects the L-to-M transition.     

Structural change of threonine 89 upon photoisomerization in bacteriorhodopsin as revealed by polarized FTIR spectroscopy.

The all-trans to 13-cis photoisomerization of the retinal chromophore of bacteriorhodopsin occurs selectively, efficiently, and on an ultrafast time scale. The reaction is facilitated by the surrounding protein matrix which undergoes further structural changes during the proton-transporting reaction cycle. Low-temperature polarized Fourier transform infrared difference spectra between bacteriorhodopsin and the K intermediate provide the possibility to investigate such structural changes, by probing O-H and N-H stretching vibrations [Kandori, Kinoshita, Shichida, and Maeda (1998) J. Phys. Chem. B 102, 7899-7905]. The measurements of [3-18O]threonine-labeled bacteriorhodopsin revealed that one of the D2O-sensitive bands (2506 cm(-1) in bacteriorhodopsin and 2466 cm(-1) in the K intermediate, in D2O exhibited 18(O)-induced isotope shift. The O-H stretching vibrations of the threonine side chain correspond to 3378 cm(-1) in bacteriorhodopsin and to 3317 cm(-1) in the K intermediate, indicating that hydrogen bonding becomes stronger after the photoisomerization. The O-H stretch frequency of neat secondary alcohol is 3340-3355 cm(-1). The O-H stretch bands are preserved in the T46V, T90V, T142N, T178N, and T205V mutant proteins, but diminished in T89A and T89C, and slightly shifted in T89S. Thus, the observed O-H stretching vibration originates from Thr89. This is consistent with the atomic structure of this region, and the change of the S-H stretching vibration of the T89C mutant in the K intermediate [Kandori, Kinoshita, Shichida, Maeda, Needleman, and Lanyi (1998) J. Am. Chem. Soc. 120, 5828-5829]. We conclude that all-trans to 13-cis isomerization causes shortening of the hydrogen bond between the OH group of Thr89 and a carboxyl oxygen atom of Asp85.     

Structural changes of water molecules during the photoactivation processes in bovine rhodopsin

Internal water molecules of rhodopsins play an important role in stabilizing the crucial ion pair comprised by the protonated retinal Schiff base and its counterion. Previous low-temperature FTIR spectroscopy of archaeal rhodopsins observed water O-D stretching vibrations at 2400-2100 cm(-1) in D(2)O, corresponding to strong hydrogen bonds. Since a water molecule bridges the protonated Schiff base and an aspartate in archaeal rhodopsins, the observed water molecules presumably hydrate the negative charges in the Schiff base region. In contrast, the FTIR spectroscopy data of bovine rhodopsin presented here revealed that there are no spectral changes of water molecules under strongly hydrogen-bonding conditions (in the range <2400 cm(-1) for O-D stretch) during the photoactivation processes. The only observed water bands were located in the >2500 cm(-1) region that corresponds to weak hydrogen bonding. These results imply that the ion pair state in vertebrate visual rhodopsins is stabilized in a manner different from that in archaeal rhodopsins. In addition, the internal water molecules that hydrate the negative charges do not play important role in the photoactivation processes of rhodopsin that involve proton transfer from the Schiff base to Glu113 upon formation of Meta II. Structural changes of the H-D exchangeable peptide amide of a beta-sheet are observed upon formation of metarhodopsin II, suggesting that motion of a beta-sheet is coupled to the proton transfer reaction from the Schiff base to its counterion.     

RNA binding efficacy of theophylline,theobromine and caffeine

The binding of naturally occurring methylxanthines such as theophylline, theobromine and caffeine to nucleic acids are reckoned to be pivotal as they are able to modulate the cellular activities. We explore the interaction of yeast RNA binding efficacy of the above xanthine derivatives by using UV absorption differential spectroscopy and Fourier Transform Infrared (FTIR) spectroscopy. Both the analyses show discrimination in their binding affinity to RNA. The differential UV-spectrum at P/D 3.3 reveals the greater RNA binding activity for theophylline (85 +/- 5%), whereas moderate and comparatively less binding activity for theobromine (45 +/- 5%) and caffeine (30 +/- 5%) and the binding activity was found to depend on concentration of the drugs. In FTIR analysis we observed changes in the amino group (NH) of RNA complexed by drugs, where the NH band is found to become very broad, indicating hydrogen bonding (H-bonding) with theophylline (3343.4 cm(-1)), theobromine (3379.8 cm(-1)) and caffeine (3343 cm(-1)) as compared to the free RNA (3341.6 cm(-1)). Furthermore in RNA-theophylline complex, it is observed that the carbonyl (C=O) vibration frequency (nu(C=O)) of both drug (nu(C=O)=1718, 1666 cm(-1)) as well as RNA (nu(C=O)=1699, 1658 cm(-1)) disappeared and a new vibration band appeared around 1703 cm(-1), indicating that the C=O and NH groups of drug and RNA are effectively involved in H-bonding. Whereas in RNA-theobromine and RNA-caffeine complexes, we found very little changes in C=O frequency and only broadening of the NH band of RNA due to complexation is observed in these groups. The changes in the vibrations of G-C/A-U bands and other bending frequencies are discussed. Thus the discrimination in the binding affinity of methylxanthines with RNA molecule shows that strong RNA binding drugs like theophylline can selectively be delivered to RNA targets of microbial pathogens having the mechanism of RNA catalysis.     

Interaction of internal water molecules with the schiff base in the L intermediate of the bacteriorhodopsin photocycle

In the photocycle of bacteriorhodopsin (BR), the first proton movement, from the Schiff base to Asp85, occurs after the formation of the L intermediate. In L, the C [double bond] N bond of the Schiff base is strained, and the nitrogen interacts strongly with its counterion. The present study seeks to detect the interaction of internal water molecules with the Schiff base in L using difference FTIR spectroscopy at 170 K. The coupled modes of the hydrogen-out-of plane bending vibrations (HOOPs) of the N-H and C(15)-H of the protonated Schiff base are detected as a broad band centered at 911 cm(-1) for BR. A set of bands at 1073, 1064, and 1056 cm(-1) for L is shown to arise from the coupling of the HOOP with the overtones of interacting water O-H vibrations. Interaction with water was shown by the decreased intensity of the HOOPs of L in H(2)(18)O and by the influence of mutants that have been shown to perturb specific internal water molecules in BR. In contrast, the HOOP band of initial BR was not affected by these mutations. In D85N, the coupled HOOP of BR is depleted, while the coupled HOOPs of L are shifted. The results indicate that the Schiff base interacts with water in the L state but in a different manner than in the BR state. Moreover, the effects of mutations suggest that cytoplasmic water close to Thr46 (Wat46) either interacts stronger with the Schiff base in L or that it is important in stabilizing another water that does.     

Hydrogen bonding alteration of Thr-204 in the complex between pharaonis phoborhodopsin and its transducer protein

Pharaonis phoborhodopsin (ppR, also called pharaonis sensory rhodopsin II, psRII) is a receptor for negative phototaxis in Natronobacterium pharaonis. It forms a 2:2 complex with its transducer protein, pHtrII, in membranes and transmits light signals through the change in the protein-protein interaction. We previously found that the ppR(K) minus ppR spectrum in D(2)O possesses vibrational bands of ppR at 3479 (-)/3369 (+) cm(-1) only in the presence of pHtrII [Furutani, Y., Sudo, Y., Kamo, N., and Kandori, H. (2003) Biochemistry 42, 4837-4842]. A D/H-unexchangeable X-H group appears to form a stronger hydrogen bond upon retinal photoisomerization in the ppR-pHtrII complex. This article aims to identify the group by use of various mutant proteins. According to the crystal structure, Tyr-199 of ppR forms a hydrogen bond with Asn-74 of pHtrII in the complex. Nevertheless, the 3479 (-)/3369 (+) cm(-1) bands were preserved in the Y199F mutant, excluding the possibility that the bands are O-H stretches of Tyr-199. On the other hand, Thr-204 and Tyr-174 form a hydrogen bond between the retinal chromophore pocket and the binding surface of the ppR-pHtrII complex. These FTIR measurements revealed that the bands at 3479 (-)/3369 (+) cm(-1) disappeared in the T204A mutant, while being shifted to 3498 (-) and 3474 (+) cm(-1) in the T204S mutant. They appear at 3430 (-)/3402 (+) cm(-1) in the Y174F mutant. From these results, we concluded that the bands at 3479 (-)/3369 (+) cm(-1) originate from the O-H stretch of Thr-204. A stronger hydrogen bond as shown by a large spectral downshift (110 cm(-1)) suggests that the specific hydrogen bonding alteration of Thr-204 takes place upon retinal photoisomerization, which does not occur in the absence of the transducer protein. Thr-204 has been known as an important residue for color tuning and photocycle kinetics in ppR. The results presented here point to an additional important role of Thr-204 in ppR for the interaction with pHtrII. Specific interaction in the complex that involves Thr-204 presumably affects the decay kinetics and binding affinity in the M intermediate.     

Modification of the phylloquinone in the A1 binding site in photosystem I studied using time-resolved FTIR difference spectroscopy and density functional theory

A phylloquinone molecule (2-methyl-3-phytyl-1,4-naphthoquinone) occupies the A1 binding site in photosystem I. Previously, we have obtained A1(-)/A1 FTIR difference spectra using labeled and unlabeled photosystem I particles and proposed assignments for many of the bands in the spectra [Sivakumar, V., Wang, R., and Hastings, G. (2005) Biochemistry 44, 1880-1893]. In particular, we suggested that a negative/positive band at 1654/1495 cm(-1) in A1(-)/A1 FTIR DS is due to a C=O/C-:O mode of the neutral/anionic phylloquinone, respectively. To test this hypothesis, we have obtained A1(-)/A1 FTIR DS for menG mutant PS I particles. In menG mutant PS I, phylloquinone in the A1 binding site is replaced with an analogue in which the methyl group at position 2 of the quinone ring is replaced with a hydrogen atom (2-phytyl-1,4-naphthoquinone). In A1(-)/A1 FTIR DS obtained using menG mutant PS I particles, we find that the 1654/1495 cm(-1) bands are upshifted by approximately 6 cm(-1). To test if such upshifts are likely for C=O/C-:O modes of neutral/anionic phylloquinone, we have used density functional theory to calculate the "anion minus neutral" infrared difference spectra for both phylloquinone and its methyl-less analogue. We have also undertaken calculations in which the C4=O carbonyl group of phylloquinone and its methyl-less analogue are hydrogen bonded (to a water or leucine molecule). We find that, irrespective of the hydrogen bonding state of the C4=O group, the C=O/C-:O modes of neutral/reduced phylloquinone are indeed expected to be upshifted by at least 6 cm(-1) upon replacement of the methyl group at position 2 with hydrogen. The calculations also suggest that certain C=C/C-:C modes of neutral/reduced phylloquinone do not shift upon replacement of the methyl group. On the basis of these calculated results, we suggest which bands in the A1(-)/A1 FTIR DS may be associated with C=C/C-:C modes of neutral/reduced phylloquinone, respectively.     

FTIR studies of internal water molecules in the Schiff base region of bacteriorhodopsin

In a light-driven proton pump protein, bacteriorhodopsin (BR), three water molecules participate in a pentagonal cluster that stabilizes an electric quadrupole buried inside the protein. Previously, low-temperature Fourier-transform infrared (FTIR) difference spectra between BR and the K photointermediate in D(2)O revealed six O-D stretches of water in BR at 2690, 2636, 2599, 2323, 2292, and 2171 cm(-)(1), while five water bands were observed at 2684, 2675, 2662, 2359, and 2265 cm(-)(1) for the K intermediate. The frequencies are widely distributed over the possible range of stretching vibrations of water, and water molecules at <2400 cm(-)(1) were suggested to hydrate negative charges because of their extremely strong hydrogen bonds. In this paper, we aimed to reveal the origin of these water bands in the K minus BR spectra by use of various mutant proteins. The water bands were not affected by the mutations at the cytoplasmic side, such as T46V, D96N, and D115N, implying that the water molecules in the cytoplasmic domain do not change their hydrogen bonds in the BR to K transition. In contrast, significant modifications of the water bands were observed for the mutations in the Schiff base region and at the extracellular side, such as R82Q, D85N, T89A, Y185F, D212N, R82Q/D212N, and E204Q. From these results, we concluded that the six O-D stretches of BR originate from three water molecules, water401, -402, and -406, involved in the pentagonal cluster. Two stretching modes of each water molecule are highly separate (300-470 cm(-)(1) for O-D stretches and 500-770 cm(-)(1) for O-H stretches), which is consistent with the previous QM/MM calculation. The small amplitudes of vibrational coupling are presumably due to strong association of the waters to negative charges of Asp85 and Asp212. Among various mutant proteins, only D85N and D212N lack strongly hydrogen-bonded water molecules (<2400 cm(-)(1)) and proton pumpimg activity. We thus infer that the presence of a strong hydrogen bond of water is a prerequisite for proton pumping in BR. Internal water molecules in such a specific environment are discussed in terms of functional importance for rhodopsins.     

Water structural changes in the bacteriorhodopsin photocycle: analysis by Fourier transform infrared spectroscopy.

The Fourier transform infrared difference spectra between light-adapted bacteriorhodopsin (BR) and its photointermediates, L and M, were analyzed for the 3750-3450-cm-1 region. The O-H stretching vibrational bands were identified from spectra upon substitution with 2H2O. Among them, the 3642-cm-1 band of BR was assigned to water by substitution with H2(18)O. By a comparison with the published infrared spectra of the water in model systems [Mohr, S.C., Wilk, W.D., & Barrow, G.M. (1965) J. Am. Chem. Soc. 87, 3048-3052], it is shown that the O-H bonds of the water in BR interact very weakly. Upon formation of L, the interaction becomes stronger. The O-H bonds of the protein side chain undergo similar changes. On the other hand, M formation further weakens the interaction of the same water molecules in BR. The appearance of a sharp band at 3486 cm-1, which was assigned tentatively to the N-H stretching vibration of the peptide bond, is unique to L. The results suggest that the water molecules are involved in the perturbation of Asp-96 in the L intermediate and that they are exerted from the protonated Schiff base which changes position upon the light-induced reaction.     

Water molecules coupled to the redox-active tyrosine Y(D) in photosystem II as detected by FTIR spectroscopy

The redox-active tyrosine YD (D2-Tyr160) in photosystem II (PSII) serves as a side-path electron donor to P680. When YD is oxidized, a proton is released from phenolic OH, and a neutral radical YD* is formed. A hydrogen bond network around YD must be deeply involved in the mechanism of the YD reaction. In this study, we have detected water molecules structurally coupled to YD by means of Fourier transform infrared (FTIR) spectroscopy. Light-induced YD*/YD FTIR difference spectrum of a hydrated film of the PSII core complexes from Thermosynechococcus elongatus showed major signals at 3636(-)/3617(+) and 3594(+)/3585(-) cm-1 in the weakly hydrogen bonded OH stretching region. These peaks downshifted by 11-12 cm-1 upon H218O substitution and almost disappeared upon H/D exchange, and hence, they were definitely assigned to the water OH vibrations. Small intramolecular couplings of 3-6 cm-1 estimated from the OH frequencies of residual HOD species in a deuterated film indicate that these OH signals arise from two different water molecules that have significantly asymmetric hydrogen bond structures. Similar OH signals were observed in PSII-enriched membranes from spinach, suggesting that two water molecules commonly exist near YD irrespective of biological species. These water molecules are coupled to YD most probably through a hydrogen bond network or one of them possibly interacts directly with YD, and thus, they may play crucial roles in the YD reaction by forming a proton-transfer pathway and tuning the redox potential of YD.     

UV Raman monitoring of histidine protonation and H-(2)H exchange in plastocyanin

UV resonance Raman bands of Cu-bound and protonated histidine residues have been detected in (2)H(2)O solutions of poplar plastocyanin. For the Cu(II) protein, slow NH-(2)H exchange of the His37 ligand was monitored via the growth of bands at 1389 and 1344 cm(-1) when Pcy was exchanged into (2)H(2)O, or via their diminution when the protein was exchanged back into H(2)O; the rate constant is 7 x 10(-4)/s at pH (p(2)H) 7.4 at room temperature. The slow exchange is attributed to imidazole H-bonding to a backbone carbonyl. Nearby bands at 1397 and 1354 cm(-1), appear and disappear within the mixing time, and are assigned to the solvent-exposed His87 ligand. The approximately 10 cm(-1) differences between His37 and His87 are attributed to the effect of H-bonding on the imidazole ring modes. The UVRR spectra of the Cu(I) protein in (2)H(2)O reveal a 1408 cm(-1) band, characteristic of NH-(2)H-exchanged histidinium, which grows in as the p(2)H is lowered. Its intensity follows a titration curve with pK(a)=4.6. This protonation is assigned to the His87 residue, whose bond to the Cu(I) is known from crystallography to be broken at low pH. As the 1408 cm(-1) band grows, a band at 1345 cm(-1) diminishes, while another, at 1337 cm(-1) stays constant. These are assigned to modes of bound His87 and His37, respectively, shifted down 7-9 cm(-1) from their Cu(II) positions.     

Water-sensitive low-frequency vibrations of reaction intermediates during S-state cycling in photosynthetic water oxidation

In photosynthetic water oxidation, two water molecules are converted to an oxygen molecule through five reaction intermediates, designated S(n) (n = 0-4), at the catalytic Mn cluster of photosystem II. To understand the mechanism of water oxidation, changes in the chemical nature of the substrate water as well as the Mn cluster need to be defined during S-state cycling. Here, we report for the first time a complete set of Fourier transform infrared difference spectra during S-state cycling in the low-frequency (670-350 cm(-1)) region, in which interactions between the Mn cluster and its ligands can be detected directly, in PS II core particles from Thermosynechococcus elongatus. Furthermore, vibrations from oxygen and/or hydrogen derived from the substrate water and changes in them during S-state cycling were identified using multiplex isotope-labeled water, including H2(18)O, D2(16)O, and D2(18)O. Each water isotope affected the low-frequency S-state cycling spectra, characteristically. The bands sensitive only to (16)O/(18)O exchange were assigned to the modes from structures involving Mn and oxygen having no interactions with hydrogen, while the bands sensitive only to H/D exchange were assigned to modes from amino acid side chains and/or polypeptide backbones that associate with water hydrogen. The bands sensitive to both (16)O/(18)O and H/D exchanges were attributed to the structure involving Mn and oxygen structurally coupled with hydrogen in a direct or an indirect manner through hydrogen bonds. These bands include the changes of intermediate species derived from substrate water during the process of photosynthetic water oxidation.     

Attenuated total reflection (ATR) Fourier transform infrared spectroscopy of dimyristoyl phosphatidylserine-cholesterol mixtures

Mixtures of cholesterol with dimyristoyl phosphatidylserine or deuterated dimyristoyl phosphatidylserine were investigated by polarized and non polarized attenuated total reflection (ATR) Fourier transform infrared (FTIR) Spectroscopy. From polarized spectra the dichroic ratios of various vibrations as a function of cholesterol were calculated. Dichroic ratios of methylene vibration (CH(2)) 2934 cm(-1) of cholesterol decreases with increase of cholesterol concentration leveling off in the region where cholesterol phase separation takes place. The orientation of deuterated methylene (CD(2)) symmetric and asymmetric bands of the deuterated dimyristoyl phosphatidylserine is influenced little by cholesterol. In the polar region of dimyristoyl phosphatidylserine no effect of cholesterol on the dichroic ratios of carbonyl (C==O) and asymmetric phosphate (PO(2)(-)) vibrations were detected. For nonpolarized spectra the broad bands in the polar region of the phospholipid were deconvoluted. The carbonyl band (C==O) in pure dimyristoyl phosphatidylserine is composed of five bands; in the presence of increasing concentrations of cholesterol conformational change of these vibrations takes place evolving into one predominant band. Similar conformational change takes place in the presence of 75 molecules water/molecule DMPS. For the asymmetric phosphate band very small shifts due to interaction with cholesterol were detected.     

Protein-bound water molecules in primate red- and green-sensitive visual pigments

Protein-bound water molecules play crucial roles in the structure and function of proteins. The functional role of water molecules has been discussed for rhodopsin, the light sensor for twilight vision, on the basis of X-ray crystallography, Fourier transform infrared (FTIR) spectroscopy, and a radiolytic labeling method, but nothing is known about the protein-bound waters in our color visual pigments. Here we apply low-temperature FTIR spectroscopy to monkey red (MR)- and green (MG)-sensitive color pigments at 77 K and successfully identify water vibrations using D(2)O and D(2)(18)O in the whole midinfrared region. The observed water vibrations are 6-8 for MR and MG, indicating that several water molecules are present near the retinal chromophore and change their hydrogen bonds upon retinal photoisomerization. In this sense, color visual pigments possess protein-bound water molecules essentially similar to those of rhodopsin. The absence of strongly hydrogen-bonded water molecules (O-D stretch at <2400 cm(-1)) is common between rhodopsin and color pigments, which greatly contrasts with the case of proton-pumping microbial rhodopsins. On the other hand, two important differences are observed in water signal between rhodopsin and color pigments. First, the water vibrations are identical between the 11-cis and 9-cis forms of rhodopsin, but different vibrational bands are observed at >2550 cm(-1) for both MR and MG. Second, strongly hydrogen-bonded water molecules (2303 cm(-1) for MR and 2308 cm(-1) for MG) are observed for the all-trans form after retinal photoisomerization, which is not the case for rhodopsin. These specific features of MR and MG can be explained by the presence of water molecules in the Cl(-)-biding site, which are located near positions C11 and C9 of the retinal chromophore. The averaged frequencies of the observed water O-D stretching vibrations for MR and MG are lower as the λ(max) is red-shifted, suggesting that water molecules are involved in the color tuning of our vision.