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Biophysical Chemistry, Biomolecules, and Biomaterials; Surfactants and Membranes

Fourier Transform Infrared Analysis of the S-State Cycle of Water Oxidation in the Microcrystals of Photosystem II Yuki Kato, Fusamichi Akita, Yoshiki Nakajima, Michihiro Suga, Yasufumi Umena, Jian-Ren Shen, and Takumi Noguchi J. Phys. Chem. Lett., Just Accepted Manuscript • DOI: 10.1021/acs.jpclett.8b00638 • Publication Date (Web): 05 Apr 2018 Downloaded from http://pubs.acs.org on April 5, 2018

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The Journal of Physical Chemistry Letters

Fourier Transform Infrared Analysis of the S-State Cycle of Water Oxidation in the Microcrystals of Photosystem II Yuki Kato1*, Fusamichi Akita2,3, Yoshiki Nakajima2, Michihiro Suga2, Yasufumi Umena2, Jian-Ren Shen2, and Takumi Noguchi1* 1: Division of Material Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan 2: Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan 3: Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 3320012, Japan

AUTHOR INFORMATION Corresponding Author *[email protected]; *[email protected]

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ABSTRACT Photosynthetic water oxidation is performed in photosystem II (PSII) through a light-driven cycle of intermediates called S states (S0–S4) at the water oxidizing center. Time-resolved serial femtosecond crystallography (SFX) has recently been applied to the microcrystals of PSII to obtain the structural information of these intermediates. However, it remains unanswered whether the reactions efficiently proceed throughout the S-state cycle retaining the native structures of the intermediates in PSII crystals. Here, we investigated the water oxidation reactions in the PSII microcrystals using flash-induced Fourier transform infrared (FTIR) difference spectroscopy. In comparison with the FTIR spectra in solution, it was shown that all the metastable intermediates in the microcrystals retain their native structures, and the efficiencies of the S-state transitions remained relatively high, although those of the S2→S3 and S3→S0 transitions were slightly lowered due possibly to some restriction of water movement in the crystals. TOC GRAPHICS


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Photosystem II (PSII) in plants and cyanobacteria is a unique enzyme that oxidizes water into molecular oxygen and protons utilizing visible light. The liberated oxygen is the main source of oxygen in the atmosphere, which sustains aerobic life on Earth. The protons released to the thylakoid lumen are used for ATP synthesis, while electrons abstracted from water are stored in NADPH; ATP and NADPH are then used to synthesize sugars from CO2. The water oxidation reaction is performed at the water oxidizing center (WOC), which is composed of the Mn4CaO5 cluster and its protein environment, located on the donor side of PSII.1–6 Light illumination on PSII induces charge separation between the special pair chlorophyll P680 and the pheophytin electron acceptor. An electron is transferred to plastoquinone electron acceptors, while the P680+ cation abstracts an electron from the Mn4CaO5 cluster via the redox-active tyrosine YZ. At the WOC, two water molecules are converted into one oxygen molecule and four protons through a light-driven cycle of five intermediates called Si states (i = 0–4).7, 8 The S1 state is the most stable intermediate in the dark, and advances to the S2 state upon single turnover electron transfer by flash illumination. Further illumination of flashes advances the S2 state to the S3 state and then to the S4 state, which is the highest oxidation state. The S4 state is a transient intermediate, and immediately relaxes to the S0 state accompanied by the release of an oxygen molecule. The fourth flash converts the S0 state to the initial S1 state to complete the S-state cycle. It is generally accepted that the transitions other than the S1→S2 transition (S0→S1, S2→S3, and S3→S0) are accompanied by proton release, 9-11 and the S2→S3 and S3→S0 (after S4 formation) transitions involve insertion of water molecules into the WOC.12-19 Recent X-ray crystallographic studies of the PSII core complexes have revealed the atomic structure of the WOC in the dark-stable S1 state at resolutions of 1.85–1.95 Å.20-22 These


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structures resolved the oxygen atoms of the Mn4CaO5 cluster and surrounding water molecules, providing an important structural basis in the researches of the water oxidation mechanism.6, 23, 24 For full understanding of the water oxidation mechanism, however, the structural information of the advanced S states is necessary. Indeed, time-resolved serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFEL), which enables to collect diffraction data before radiation damage,25 has been applied to the microcrystals of PSII.26–30 In the SFX experiments, snapshot diffraction images from the flash-illuminated PSII crystals were taken to detect the structural changes during the S-state transitions. The SFX studies with resolutions lower than 4.5 Å did not show any specific changes upon illumination of one to three flashes.26–28 Recent two reports with resolutions around 2.3 Å29, 30 showed some specific changes by two flashes. Young et al.29 observed slight changes in the O4 and Mn4 positions, but did not find evidence for binding of a new water to Mn1. In contrast, Suga et al.30 demonstrated the appearance of a new oxygen atom close to O5 between Mn1 and Mn4 upon two flashes, suggesting water insertion in the S2→S3 transition for O=O bond formation. In addition, they observed the displacement of a water molecule near O4 and the concomitant movement of another water molecule hydrogenbonded with O4 toward O4. Although the exact reason for the sharp contrast between these two SFX works is unknown, Wang et al.31 recently pointed out insufficient data processing procedures in ref. 29 from the analysis of the difference Fourier maps based on the QM/MM calculations. In SFX studies of the intermediates of the WOC in the PSII crystals, it is crucial to know whether the flash-induced S-state transitions advance with efficiencies as high as PSII complexes in solution. Another important but unanswered question is whether the intermediates of the WOC retain their native structures or have somewhat modified structures in crystals.


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To answer these questions, light-induced Fourier transform infrared (FTIR) difference spectroscopy is a very powerful method. It can detect subtle structural changes at atomic level, involving changes in hydrogen bond and protonation structures, of cofactors and surrounding protein moieties in large protein complexes.32–34 Extensive studies using this spectroscopy have been performed to investigate the molecular mechanism of water oxidation in PSII.35–39 FTIR difference spectra of the WOC during the S-state cycle upon illumination of successive flashes exhibited specific signals reflecting the structural changes in amino acid side chains, polypeptide main chains, and water molecules as well as the Mn4CaO5 cluster itself. In addition, the analysis of the oscillation patterns of the FTIR signals provided the efficiencies of the S-state transitions.11, 12, 40–42 In the recent SFX study by Suga et al.,30 we estimated the population of the S3 state after illumination of two flashes on the PSII crystals using FTIR difference spectroscopy. In the present study, we further analyzed all the transitions in the S-state cycle of the WOC in PSII microcrystals by detecting the FTIR difference spectra upon illumination of successive flashes. By comparing the obtained spectra with the spectra of PSII complexes in solution, we discuss the structures and reactions of the WOC in PSII microcrystals. Flash-induced FTIR difference spectra were measured using the microcrystals of the PSII core complexes from Thermosynechococcus vulcanus deposited on the surface of a silicon prism of the attenuated total reflectance (ATR) accessory at 10 °C (for details, see Materials and Methods in Supporting Information). The microcrystals were in a buffer (pH 6.0) containing 7% polyethylene glycol (PEG) 1450. Potassium ferricyanide (20 mM) was also added to the sample as an exogenous electron acceptor. ATR-FTIR difference spectra of the S-state cycle of the WOC were measured by applying 6 successive flashes (10-s intervals) to the microcrystals (Figure 1, red lines). The spectra were compared with the control spectra of the PSII complexes


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in solution measured by applying 12 successive flashes (Figure 1, black lines; all spectra by 12 flashes are shown in Figure S1). A larger number of flashes were applied to this solution sample to estimate the transition efficiencies from the oscillation patterns of the FTIR signals (see below). These control spectra of the PSII complexes from T. vulcanus (Figure 1, black lines) are very similar to the spectra of the S-state cycle reported previously,12, 40, 43–46 and the spectra upon

c

1800

1700

1600

1361

1260

1329

1254

1343

1255 1255 1262 1253

1342 1356

1396

1500

1328

1397

1364 1358

1434 1417 1401

1445

1354 1344 1324

1435 1419 1445

1443

1525 1510 1523 1511

1508

1510

1543

1563

1543

1640

1550

1586 1562

1614

1662 1650

1538

1659 1648 1640

1687 1678 1695

1686

1687

f

1667

1675

e

1668 1651 1651 1634

d

-4

1357

1398 1396

1417

1.0x10 1400

1514

1446

1538 1523

1436

1507

1586

1550 1544

1541

1614 1652 1641

1661

1676

1687

b

1561

1686 1669 1661

1667

1676

a

1634

1651

the 1st, 2nd, 3rd, and 4th flashes virtually represent the S1→S2, S2→S3, S3→S0, and S0→S1

A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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1400

1300

1200

-1

Wavenumber/cm

Figure 1. FTIR difference spectra of the S-state cycle of the PSII core complexes from T. vulcanus in the microcrystals (red lines), solution (black lines), and solution in the presence of 7% PEG (green lines) upon the (a) 1st, (b) 2nd, (c) 3rd, (d) 4th, (e) 5th, and (f) 6th flashes. Spectra were scaled based on the intensities of the 1st-flash spectra.


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transitions, respectively. Bands in the 1450–1300 cm−1 region have been assigned to the symmetric COO− stretching vibrations of the carboxylate groups around the Mn4CaO5 cluster,47– 49

while bands in the 1700–1600 and 1600–1500 cm−1 regions mainly arise from the amide I and

amide II/asymmetric COO− vibrations, respectively48 (for detailed interpretation of the FTIR spectra of S-state transitions, see previous review articles33, 35-39). The spectral features of the PSII crystals at the 1st and 2nd flashes were virtually identical to those of the control sample in solution (Figure 1a, b). The overall intensity of the 2nd-flash spectrum was slightly smaller than that of the control spectrum when the spectral intensities were normalized based on the 1st-flash spectra. The 3rd- and 4th-flash spectra of the PSII crystals also exhibited features similar to the corresponding spectra of the PSII solution (Figure 1c, d). However, the overall intensities of these spectra of the crystals were apparently smaller than those of the solution spectra. The reduced intensities after the 3rd flash in the crystals are clearly shown in the plot of flash-number dependence of the intensity difference between 1400 and 1436 cm−1 in the COO− region (Figure 2). Because the crystal sample included 7% PEG to retain the crystals, there could be a possibility that the presence of PEG somehow inhibited the advancement of the higher S-state transitions. To examine the effect of PEG, we measured the spectra of the PSII complexes in solution in the presence of 7% PEG in the similar way to the control solution sample (Figure 1, green lines; all spectra by 12 flashes are shown in Figure S2). The spectra were very similar to those of the solution sample in the absence of PEG, except that the overall intensity at the 3rd flash is only slightly smaller. This is also expressed in the flash-number dependence of the relative intensity in the COO− bands in comparison with the plot of the control sample (Figure 2).


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1.0

Relative intensity

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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0.5

0.0

-0.5

-1.0 1

2

3

4

5

6

Flash number

Figure 2. Flash-number dependence of the relative intensities of the COO− stretching bands in the FTIR difference spectra of the PSII complexes in the microcrystals (red circles), solution (black triangles), and solution in the presence of 7% PEG (green inverse triangles). The intensity difference between 1400 and 1436 cm−1 in the spectra in Figure 1 was plotted against the flash number. The amplitude at the 1st flash was adjusted to −1.0.

The relaxation rate of the S3/S2 states, which was measured by successive spectral detection after illumination of two flashes (Figure S3), was much faster in the crystals (t1/2 = ~50 s) than in solution (t1/2 = ~120 s). The rate was only slightly faster in the solution in the presence of 7% PEG (t1/2 = ~100 s), and hence the accelerated relaxation in the crystals is not ascribed to the presence of PEG in the sample. The S3/S2 states should be relaxed by reduction by ferrocyanide, which is formed from ferricyanide by electron transfer from the quinone electron acceptors. Therefore, the faster decay in the PSII crystals than in the solutions may be caused by faster reduction of the S3/S2 states due to a higher concentration of ferrocyanide around PSII, which may be realized by restriction of the diffusion of ferrocyanide within the crystal lattice. The difference in the relaxation rate between the crystal and solution samples, however, confirms that the observed spectra of the microcrystals are not attributed to PSII proteins dissolved into solution from the crystal surface.


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The efficiencies of the individual S-state transitions in the PSII sample can be estimated by simulation of the oscillation pattern of the intensities of the CN stretching bands of ferricyanide/ferrocyanide as shown by Suzuki et al.42 Using this method (see Supporting Information for details), the efficiencies of the S1→S2, S2→S3, S3→S0, and S0→S1 transitions in the control solution sample were estimated to be 0.94 ± 0.04, 0.90 ± 0.04, 0.85 ± 0.04, and 0.94 ± 0.02, respectively, from the oscillation pattern of 12 flashes (Table 1, Figure S4A, B). These values are consistent with the previous estimation using the PSII core complexes from T. elongatus.42 The average of these values, 0.90 ± 0.02, was in good agreement with the average efficiency, 0.89 ± 0.02, obtained from the oscillation pattern of the COO− bands at 1436/1400 cm−1 (Table 1, Figure S4C), confirming the proper estimation of the individual efficiencies. Similarly, the S-state transition efficiencies of the solution sample containing 7% PEG was estimated to be 0.86 ± 0.09, 0.88 ± 0.09, 0.75 ± 0.11, and 0.90 ± 0.05 for the S1→S2, S2→S3, S3 →S0, and S0→S1 transitions, respectively (Table 1, Figure S5A, B). Again, the average value, 0.85 ± 0.04, is in agreement with the average efficiency, 0.85 ± 0.02, estimated using the COO− bands (Table 1, Figure S5C). These values are slightly lower than the efficiencies of the control solution sample, which could be due to the exclusion of some water molecules from PSII proteins as the effect of PEG.

For the crystal sample, the same method could not be used for accurate estimation of the individual efficiencies, because the oscillation pattern was not fitted well after 6 flashes when 12 flashes were applied to the crystals (data not shown). This may be due to a rather limited supply of ferricyanide as an electron acceptor in the crystal. The S-state transition efficiencies of the crystal sample were hence estimated by spectral fitting using the control spectra of the solution


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Table 1: Efficiencies of the S-state transitions in the PSII complexes from T. vulcanus in microcrystals and solutions estimated from the flash-induced FTIR difference spectra sample

method

S1→S2

S2→S3

S3→S0

S0→S1

average

solution

ferri/ferroa

0.94 ± 0.04

0.90 ± 0.04

0.85 ± 0.04

0.94 ± 0.02

0.90 ± 0.02d

COO−b

–

–

–

–

0.89 ± 0.02

ferri/ferroa

0.86 ± 0.09

0.88 ± 0.09

0.75 ± 0.11

0.90 ± 0.05

0.85 ± 0.04d

COO−b

–

–

–

–

0.85 ± 0.02

solution (+7% PEG)

crystal spectral 0.74 ± 0.02d 0.83 ± 0.03 0.65 ± 0.03 0.58 ± 0.03 0.88 ± 0.04 (+7% PEG) fittingc a Efficiencies of the individual S-state transitions estimated using ferricyanide/ferrocyanide bands. b

Average efficiency estimated using COO− bands. cEfficiencies of the individual S-state transitions

estimated by spectral fitting using the spectra of the solution sample. dAverage of the efficiencies of the four S-state transitions.

sample following the method described previously12, 36 with slight modification (see Supporting Information for details). The ith-flash spectra in the PSII crystal, fi() (i = 1–4), were fitted with the linear combinations of the control spectra at the 1st–4th flashes in the solution sample, Fj() (j = 1–4):

1

4

where cij are the coefficients of linear combination, ai and bi are coefficients for baseline correction. The efficiencies of the S1→S2, S2→S3, S3→S0, and S0→S1 transitions, α1, α2, α3, and α4, respectively, can be expressed as: α1 = 1 − {c21 + c22(1 − α1’)}/c11 α2 = α2’(c22/c11)


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α3 = α3’(c33/c22) α4 = α4’(c44/c33) where α1’, α2’, α3’, and α4’ are the efficiencies of the S1→S2, S2→S3, S3→S0, and S0→S1 transitions, respectively, in the control solution sample. Note that α1 can be obtained with the above equation even if the scaling factor of the control spectra based on the amount of the active centers is unknown (see Supporting Information). The coefficients were obtained by leastsquares fitting of the spectra in the region of 1600–1200 cm−1 (Figure 3). The region higher than 1600 cm−1 was excluded from the fitting region, because strong absorption around 1650 cm−1 due to the amide I and water bending vibrations increases the noise level and affects the spectral shapes. It is shown that all the four spectra of the crystals (Figure 3, red solid lines) were fitted well using the control spectra of the PSII solution throughout the fitting region (fitting spectra are shown in black solid lines, and the individual components are shown in dotted lines). The efficiencies of 0.83 ± 0.03, 0.65 ± 0.03, 0.58 ± 0.03, and 0.88 ± 0.04 were obtained for the S1→ S2, S2→S3, S3→S0, and S0→S1 transitions, respectively, with an average efficiency of 0.74 ± 0.02 (Table 1). The efficiencies were decreased more significantly in the S2→S3 and S3→S0 transitions than the S1→S2 and S0→S1 transitions by crystallization. Because of the relatively good efficiency in the S0→S1 transition at the 4th flash, the lower efficiencies of the S2→S3 and S3→S0 transitions by the 2nd and 3rd flashes are not ascribed to the limited supply of the electron acceptor (ferricyanide) at the QB site. In addition, because the extent of the efficiency decreases in the crystals was larger than that in the solution sample with 7% PEG (Table 1), the effects are not directly ascribed to the presence of 7% PEG in the crystal sample. The larger effects on the S2→S3 and S3→S0 transitions are reminiscent of the previous results of the


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a

5x10

-5

b

A

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c

d

1600

1500

1400

1300 -1

1200

Wavenumber/cm

Figure 3. Least-squares fitting of the FTIR difference spectra of the PSII microcrystals upon the (a) 1st, (b) 2nd, (c) 3rd, and (d) 4th flashes as linear combinations of the standard spectra of the PSII solution (1st–4th flashes). Red solid lines: spectra of the microcrystals; black solid lines: fitting spectra as sums of the spectral components (blue, green, magenta, and orange dotted lines represent the 1st, 2nd, 3rd and 4th-flash spectra, respectively, in solution).

dehydration effects on the efficiencies of the S-state transitions.12 In the latter study, it was suggested that insertion of water substrate to the WOC takes place in these transitions, although the inserted water molecules are not necessarily used in the immediate cycle.12, 13 A number of theoretical studies have also suggested that water substrate is inserted in the S2→S3 and S4→S0 transitions, accompanying rearrangement of water molecules around the Mn4CaO5 cluster.14-19 Furthermore, molecular dynamics simulations have demonstrated drastic movement of water molecules through water channels in the PSII proteins for water entrance.50-52 The lower efficiencies of the S2→S3 and S3→S0 transitions in the PSII crystals may thus suggest that the


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movement of water molecules in PSII proteins is rather restricted in the crystals. In turn, the present observation may support the view that the S2→S3 and S3→S0 (after S4 formation) transitions involve a water insertion process. FTIR difference spectroscopy is very sensitive to subtle structural changes in the active sites of proteins. Changes in bond lengths in the order of 0.001 Å often provide clear frequency shifts of corresponding vibrations.49, 53 In particular, the COO− vibrations of carboxylate groups around the Mn4CaO5 cluster are significantly coupled,49 and hence even slight changes in the environment of the Mn4CaO5 cluster will affect the spectral shapes in the 1600–1300 cm−1 region, where asymmetric and symmetric COO− bands mainly appear in the FTIR spectra of the S-state transitions.44–49 Thus, the above result that the spectral features in the 1600–1200 cm−1 region of all the S-state transitions in the PSII crystals were well reproduced by the linear combinations of the 1st–4th flash spectra of the solution sample (Figure 3) indicates that the structures of all the metastable intermediates (S0–S3) of the WOC are virtually unaffected by crystallization. This may be rationalized by the fact that PSII is a membrane protein and the WOC is located deep inside the large protein complex. This further indicates that SFX detection of the intermediates during the S-state cycle will provide the information of their native structures. In our previous SFX work with FTIR estimation of the S3 population after two flashes,30 a post-crystallization procedure was conducted, in which the concentrations of PEG1450 + PEG monomethyl ether 5000, and glycerol were increased stepwise to 18% and 22%, respectively, to obtain better diffraction data. The slightly lower population of the S3 state (0.46 ± 0.03) than the present work (0.55 ± 0.03) could be due to this post-crystallization procedure. Optimizing the post-crystallization condition that ensures both of the high X-ray crystallographic resolution and


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high efficiencies of individual S-state transitions will be crucial in future SFX studies to resolve the intermediate structures beyond S3. In conclusion, FTIR characterization of the PSII microcrystals showed that all of the Sstate intermediates (S0–S3) of the WOC in the PSII crystals retain their native structures. It was also found that the efficiencies of the S0→S1 and S1→S2 transitions in the PSII crystals were kept relatively high, although those of the S2→S3 and S3→S0 transitions were slightly lowered by crystallization due possibly to some restriction of water movement in the crystal. The present results indicate that future SFX investigations of the intermediates during the S-state cycle using PSII microcrystals are promising to unravel the molecular mechanism of photosynthetic water oxidation.

ASSOCIATED CONTENT Supporting Information. Materials and Methods; Figures showing FTIR difference spectra of the PSII solution upon 1st12th flashes, FTIR difference spectra of the PSII solution +7% PEG upon 1st-12th flashes, relaxation of the S3/S2 states in the PSII samples, estimation of the efficiencies of the S-state transitions in the PSII solution, estimation of the efficiencies of the S-state transitions in the PSII solution +7% PEG. The supporting information is available free of charge via the Internet at http://pubs.acs.org.


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AUTHOR INFORMATION Notes The authors declare no competing financial interests. ACKNOWLEDGMENT This study was supported in part by JSPS KAKENHI Grant Numbers JP16K17854 (Y.K.), JP16K21181 (F.A.), JP17H05884, JP16H06162 (M.S.), JP16KT0058, JP15H05588 (Y.U.), JP17H06433 (J.R.S. and T.N.), JP17H0643419, JP24000018 (J.R.S.), JP17H06435, JP17H03662 (T.N.), an Asahi Glass Foundation (F.A.), a Kato Memorial Bioscience Foundation (F.A.), and PRESTO from JST Grant No JPMJPR16P1 (F.A.).

REFERENCES (1) Debus, R. J. The manganese and calcium ions of photosynthetic oxygen evolution. Biochim. Biophys. Acta 1992, 1102, 269–352. (2) McEvoy, J. P.; Brudvig, G. W. Water-splitting chemistry of photosystem II. Chem. Rev. 2006, 106, 4454–4483. (3) Dau, H.; Haumann, M. The manganese complex of photosystem II in its reaction cycle: Basic framework and possible realization at the atomic level. Coord. Chem. Rev. 2008, 252, 273– 295. (4) Cox, N.; Messinger, J. Reflections on substrate water and dioxygen formation. Biochim. Biophys. Acta 2013, 1827, 1020–1030. (5) Yano, J.; Yachandra, V. Mn4Ca cluster in photosynthesis: Where and how water is oxidized to dioxygen. Chem. Rev. 2014, 114, 4175–4205.


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(6) Shen, J.-R. The structure of photosystem II and the mechanism of water oxidation in photosynthesis. Annu. Rev. Plant Biol. 2015, 66, 23–48. (7) Joliot, P.; Barbieri, G.; Chabaud, R. Model of the System II photochemical centers. Photochem. Photobiol. 1969, 10, 309–329. (8) Kok, B.; Forbush, B.; McGloin, M. Cooperation of charges in photosynthetic O2 evolution-I. A linear four step mechanism. Photochem. Photobiol. 1970, 11, 457–475. (9) Förster, V.; Junge, W. Stoichiometry and kinetics of proton release upon photosynthetic water oxidation. Photochem. Photobiol. 1985, 41, 183–190. (10) Schlodder, E.; Witt, H. T. Stoichiometry of proton release from the catalytic center in photosynthetic water oxidation. J. Biol. Chem. 1999, 274, 30387–30392. (11) Suzuki, H.; Sugiura, M.; Noguchi, T. Monitoring proton release during photosynthetic water oxidation in photosystem II by means of isotope-edited infrared spectroscopy. J. Am. Chem. Soc. 2009, 131, 7849–7857. (12) Noguchi, T.; Sugiura, M. Flash-induced FTIR difference spectra of the water oxidizing complex in moderately hydrated photosystem II core films: Effect of hydration extent on Sstate transitions. Biochemistry 2002, 41, 2322–2330. (13) Noguchi T. FTIR detection of water reactions in the oxygen-evolving centre of photosystem II. Phil. Trans. R. Soc. B 2008, 363, 1189–1195. (14) Siegbahn, P. E. M. Mechanisms for proton release during water oxidation in the S2 to S3 and S3 to S4 transitions in photosystem II. Phys. Chem. Chem. Phys. 2012, 14, 4849–4856. (15) Siegbahn, P. E. M. Water oxidation mechanism in photosystem II, including oxidations, proton release pathways, O-O bond formation and O2 release. Biochim. Biophys. Acta, Bioenerg. 2013, 1827, 1003–1019. (16) Narzi, D.; Bovi, D.; Guidoni, L. Pathway for Mn-cluster oxidation by tyrosine-Z in the S2 state of photosystem II. Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 8723−8728.


16

Page 17 of 21 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(17) Retegan, M.; Krewald, V.; Mamedov, F.; Neese, F.; Lubitz, W.; Cox, N.; Pantazis, D. A. A five-coordinate Mn(IV) intermediate in biological water oxidation: spectroscopic signature and a pivot mechanism for water binding. Chem. Sci. 2016, 7, 72-84. (18) Guo, Y.; Li, H.; He, L.-L.; Zhao, D.-X.; Gong, L.-D.; Yang, Z.-Z. The open-cubane oxooxyl coupling mechanism dominates photosynthetic oxygen evolution: a comprehensive DFT investigation on O-O bond formation in the S4 state. Phys. Chem. Chem. Phys. 2017, 19, 13909−13923. (19) Guo, Y.; Li, H.; He, L.-L.; Zhao, D.-X.; Gong, L.-D.; Yang, Z.-Z. Theoretical reflections on the structural polymorphism of the oxygen-evolving complex in the S2 state and the correlations to substrate water exchange and water oxidation mechanism in photosynthesis. Biochim. Biophys. Acta, Bioenerg. 2017, 1858, 833–846. (20) Umena, Y.; Kawakami, K.; Shen, J.-R.; Kamiya, N. Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å. Nature 2011, 473, 55–60. (21) Suga, M.; Akita, F.; Hirata, K.; Ueno, G.; Murakami, H.; Nakajima, Y.; Shimizu, T.; Yamashita, K.; Yamamoto, M.; Ago, H.; Shen, J.-R. Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses. Nature 2015, 517, 99–103. (22) Tanaka, A.; Fukushima, Y.; Kamiya, N. Two different structures of the oxygen-evolving complex in the same polypeptide frameworks of photosystem II. J. Am. Chem. Soc. 2017, 139, 1718–1721. (23) Askerka, M.; Brudvig, G. W.; Batista, V. S. The O2-evolving complex of photosystem II: Recent insights from quantum mechanics/molecular mechanics (QM/MM), extended X‑ray absorption fine structure (EXAFS), and femtosecond X‑ray crystallography data. Acc. Chem. Res. 2017, 50, 41–48. (24) Pérez-Navarro, M.; Neese, F.; Lubitz, W.; Pantazis, D. A., Cox, N. Recent developments in biological water oxidation. Curr. Opin. Chem. Biol. 2016, 31, 113–119.


17


Page 18 of 21

(25) Neutze, R.; Wouts, R.; van der Spoel, D.; Weckert, E.; Hajdu, J. Potential for biomolecular imaging with femtosecond X-ray pulses. Nature 2000, 406, 752–757. (26) Kern, J.; Alonso-Mori, R.; Tran, R.; Hattne, J.; Gildea, R. J.; Echols, N.; Glockner, C.; Hellmich, J.; Laksmono, H.; Sierra, R. G. et al. Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Science 2013, 340, 491–495. (27) Kupitz, C.; Basu, S.; Grotjohann, I.; Fromme, R.; Zatsepin, N. A.; Rendek, K. N.; Hunter, M. S.; Shoeman, R. L.; White, T. A.; Wang, D. et al. Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser. Nature 2014, 513, 261–265. (28) Kern, J.; Tran, R.; Alonso-Mori, R.; Koroidov, S.; Echols, N.; Hattne, J.; Ibrahim, M.; Gul, S.; Laksmono, H.; Sierra, R. G. et al. Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nat. Commun. 2014, 5, 4371. (29) Young, I. D.; Ibrahim, M.; Chatterjee, R.; Gul, S.; Fuller, F. D.; Koroidov, S.; Brewster, A. S.; Tran, R.; Alonso-Mori, R.; Kroll, T. et al. Structure of photosystem II and substrate binding at room temperature. Nature 2016, 540, 453–457. (30) Suga, M.; Akita, F.; Sugahara, M.; Kubo, M.; Nakajima, Y.; Nakane, T.; Yamashita, K.; Nakabayashi, M.; Umena, Y.; Yamane, T. et al. Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL. Nature 2017, 543, 131–135. (31) Wang, J.; Askerka, M.; Brudvig, G. W.; Batista, V. S. Insights into photosystem II from isomorphous difference Fourier maps of femtosecond X‑ray diffraction data and quantum mechanics/molecular mechanics structural models. ACS Energy Lett. 2017, 2, 397–407. (32) Mäntele, W. Reaction-induced infrared difference spectroscopy for the study of protein function and reaction mechanisms. Trends Biochem. Sci. 1993, 18, 197–202. (33) Noguchi, T.; Berthomieu, C. Molecular analysis by vibrational spectroscopy. Photosystem II: The Light-Driven Water:Plastoquinone Oxidoreductase; Wydrzynski, T., Satoh, K., Eds.;


18

Page 19 of 21 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Advances in Photosynthesis and Respiration; Springer: Dordrechet, The Netherlands, 2005; Vol. 22, pp. 367–387. (34) Berthomieu, C.; Hienerwadel, R. Fourier transform infrared (FTIR) spectroscopy. Photosynth. Res. 2009, 101, 157–170. (35) Debus, R. J. Protein ligation of the photosynthetic oxygen-evolving center. Coord. Chem. Rev. 2008, 252, 244–258. (36) Noguchi, T. Fourier transform infrared analysis of the photosynthetic oxygen-evolving center. Coord. Chem. Rev. 2008, 252, 336–346. (37) Chu, H.-A. Fourier transform infrared difference spectroscopy for studying the molecular mechanism of photosynthetic water oxidation. Front. Plant Sci. 2013, 4, 146. (38) Debus, R. J. FTIR studies of metal ligands, networks of hydrogen bonds, and water molecules near the active site Mn₄CaO₅ cluster in photosystem II. Biochim. Biophys. Acta, Bioenerg. 2015, 1847, 19–34. (39) Noguchi, T. Fourier transform infrared difference and time-resolved infrared detection of the electron and proton transfer dynamics in photosynthetic water oxidation. Biochim. Biophys. Acta, Bioenerg. 2015, 1847, 35–45. (40) Noguchi, T.; Sugiura, M. Flash-induced Fourier transform infrared detection of the structural changes during the S-state cycle of the oxygen-evolving complex in photosystem II. Biochemistry 2001, 40, 1497–1502. (41) Suzuki, H.; Sugiura, M.; Noguchi, T. pH dependence of the flash-induced S-state transitions in the oxygen-evolving enter of photosystem II from Thermosynechococcus elongatus as Revealed by Fourier Transform Infrared Spectroscopy Biochemistry 2005, 44, 1708–1718. (42) Suzuki, H.; Sugiura, M.; Noguchi, T. Determination of the miss probabilities of individual S-state transitions during photosynthetic water oxidation by monitoring electron flow in photosystem II using FTIR spectroscopy. Biochemistry 2012, 51, 6776–6785.


19


Page 20 of 21

(43) Hillier, W.; Babcock, G. T. S-state dependent Fourier transform infrared difference spectra for the photosystem II oxygen evolving complex. Biochemistry 2001, 40, 1503–1509. (44) Debus, R. J. Evidence from FTIR difference spectroscopy that D1-Asp61 influences the water reactions of the oxygen-evolving Mn4CaO5 cluster of photosystem II. Biochemistry 2014, 53, 2941–2955. (45) Kimura, Y.; Mizusawa, N.; Ishii, A.; Ono, T. FTIR detection of structural changes in a histidine ligand during S-state cycling of photosynthetic oxygen-evolving complex. Biochemistry 2005, 44, 16072–16078. (46) Schuth, N.; Liang, Z. Y.; Schönborn, M.; Kussicke, A.; Assunção, R.; Zaharieva, I.; Zilliges, Y.; Dau, H. Inhibitory and non-inhibitory NH3 binding at the water-oxidizing manganese complex of photosystem II suggests possible sites and a rearrangement mode of substrate water molecules. Biochemistry 2017, 56, 6240–6256. (47) Noguchi, T.; Ono, T.; Inoue, Y. Direct detection of a carboxylate bridge between Mn and Ca2+ in the photosynthetic oxygen-evolving center by means of Fourier transform infrared spectroscopy. Biochim. Biophys. Acta 1995, 1228, 189–200. (48) Noguchi, T.; Sugiura, M. Analysis of flash-induced FTIR difference spectra of the S-state cycle in the photosynthetic water-oxidizing complex by uniform 15N and 13C isotope labeling. Biochemistry 2003, 42, 6035–6042. (49) Nakamura, S.; Noguchi, T. Quantum mechanics/molecular mechanics simulation of the ligand vibrations of the water-oxidizing Mn4CaO5 cluster in photosystem II. Proc. Natl. Acad. Sci. U. S. A. 2016, 113, 12727–12732. (50) Vassiliev, S.; Comte, P.; Mahboob, A. ; Bruce, D. Tracking the flow of water through photosystem II using molecular dynamics and streamline tracing. Biochemistry 2010, 49, 1873–1881. (51) Ogata, K.; Yuki, T.; Hatakeyama, M.; Uchida, W.; Nakamura, S. All-atom molecular dynamics simulation of photosystem II embedded in thylakoid membrane. J. Am. Chem. Soc. 2013, 135, 15670–15673.


20

Page 21 of 21 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(52) Sakashita, N.; Watanabe, H. C.; Ikeda, T.; Saito, K.; Ishikita, H. Origins of water molecules in the photosystem II crystal structure. Biochemistry 2017, 56, 3049–3057. (53) Takei, K.; Takahashi R.; Noguchi, T. Correlation between the hydrogen-bond structures and the C=O stretching frequencies of carboxylic acids as studied by density functional theory calculations: Theoretical basis for interpretation of infrared bands of carboxylic groups in proteins. J. Phys. Chem. B 2008, 112, 6725–6731.


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