Article pubs.acs.org/JPCB
Theoretical Study on the Role of Ca2+ at the S2 State in Photosystem II Jingxiu Yang,† Makoto Hatakeyama,‡ Koji Ogata,‡ Shinichiro Nakamura,*,‡ and Can Li*,† †
State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, 116023 Dalian, People’s Republic of China ‡ Nakamura Laboratory, RIKEN Research Cluster for Innovation, 351-0198 Wako, Japan S Supporting Information *
ABSTRACT: In photosynthesis, calcium is crucial for oxygen evolution. In the absence of Ca2+, the Kok cycle has been proven to stop at S2 with Yz•. To explore the reason, photosystem II (PSII) S2 models (in total 32452 atoms) with different metal ions (Ca2+, Sr2+, and K+) or without Ca2+ involved in the oxygen evolution complex (OEC) have been theoretically studied based on the previous dynamic study of PSII. It is found that the portion of the Mn1 d-orbital decreases in the highest occupied molecular orbitals for Ca2+depleted PSII. This feature is unfavorable for the electron transfer from the OEC to the Yz•. Furthermore, the proton donor−acceptor distance was found elongated by the alternation of the binding water in the absence of Ca2+. The isolated vibrational modes of the key water molecules along the path and their high frequency of the OH stretching modes also suggested the difficulty of the proton transfer from the OEC toward the proton exit channel. This work provides one mechanistic explanation for the inactivity of Ca2+-depleted PSII.
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were all suggested able to replace Ca2+ yet were inhibitory for the oxygen evolution reaction in PSII.12−16 Except Ca2+, only Sr2+reconstructed PSII could recover about 50% steady activity.5,7,16 The reason for the mentioned change was once attributed to the different pKa of the metal ions, which acted as Lewis acids, binding the substrate water and tuning its reactivity.17 Besides, it has been recently deduced that Ca2+ rather than other metal ions maintains the correct configuration of the surrounding water network by pulsed EPR and FTIR spectroscopy.18,19 These findings all imply that the role of Ca2+ might relate to the electron transfer (ET) and proton transfer (PT) for the long-range oxidization in PSII. However, systematic investigation or further understanding of this issue is scarce. To explore the exact working mechanism of Ca2+, a Ca-depleted (inhibitory) S2 model and Ca2+ (active), Sr2+ (active), and K+ (inhibitory) substituted S2 models based on the previous dynamic study20 were optimized and analyzed by QM/MM method. We have found that Ca2+ or other substituted metal ions have influence on the geometrical and electronic structure of the OEC that is closely related to the ET and PT.
INTRODUCTION Nature’s light-driven water oxidization is performed by the oxygen evolving complex (OEC) of photosystem II (PSII). Water is decomposed into protons, electrons, and molecular oxygen while the OEC passes through five intermediate states of the so-called Kok cycle.1 Each electron release in the Kok cycle is initiated by the oxidation of tyrosine (Yz), which consequently oxidizes the OEC. The complex consists of an oxo-bridged Mn4 cluster containing primarily Mn(III) and Mn(IV) ions and one Ca2+ ion.2−4 This Ca2+ plays the crucial role in oxygen evolution; without Ca2+, the OEC could not achieve the S3 state. The study about the role of Ca2+ could go back to the 1980s.5−7 In 1984, Ghanotakis et al. found that high-salt-treated PSII produced 80% inhibition of O2 evolution.6 The addition of Ca2+ back to the salt-washed PSII can effectively recover the O2 evolution activity.6 Later, it was found that the inhibition could reach 91% in the absence of Ca2+, when the pH value was low enough.7 Boussac et al. and Sivaraja et al. reported the observation of a broad EPR signal centered at g = 2.0 for Ca-depleted samples at “S3”.8,9 Tang et al. proved that the “S3” EPR signal arose from the Yz• radical by pulsed ENDOR spectroscopy and ESEEM studies on citrate-treated PSII.10 Latimer and his coworkers reported that there was no evidence of Mn oxidization in the “S2−S3” transition for Ca-depleted PSII according to their Mn K-edge X-ray absorption spectroscopy study.11 In other words, illumination of Ca2+-depleted PSII allowed the S state to advance to an intermediate step where the CaMn4O5 cluster remained in the S2 state, yet Yz was oxidized and deprotonated to be a neutral Yz• radical. Other possible metal ion candidates to replace Ca2+ have been proposed and examined. Alkali metal, transition metal, and lanthanides ions such as K+, Cs+, Na+, Mn2+, Cd2+, and so forth © XXXX American Chemical Society
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COMPUTATIONAL MODELS AND METHOD The PSII model in this work is based on the recent X-ray crystal structure of PSII at 1.9 Å resolution,3 with 418 atoms in the QM layer and a total of 32452 atoms in the model. To obtain the well-optimized structure, a large QM layer was determined including the CaMn4O5, the directly coordinated first shell, part of the connected second-shell amino acids, and the crystal water Received: June 13, 2014 Revised: October 27, 2014
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Figure 1. Model of the QM layer for S2−Ca with different amino acids colored differently.
III−IV−IV−IV and IV−IV−IV−III were taken into account. Agreement had been reached that no proton release occurs during S1−S2 transition.2,4,21,22 Therefore, no proton release model has been adopted for S2. According to our calculation, the III−IV−IV−IV structure turned out to be energetically more stable than the IV−IV−IV−III structure by 6.92 kcal mol−1 shown in Table 1. Thus, we focus on the analysis of the S2
molecules within the structure. As shown in Figure 1, different amino acids are colored separately. Besides the OEC, our models contain the seven directly coordinated amino acids (all from chain D1, unless otherwise indicated) such as Asp170, Glu189, His332, Glu333, Asp342, Ala344, and CP43-Glu354. In addition, the Asp61, His337, and CP43-Arg357 are also included because they form hydrogen bonds with several oxygen atoms in the OEC. Certainly, the models contain His190, Tyr161 (Yz), and the hydrogen-bonded water molecules because of the H-bond network surrounding the OEC. Moreover, the two chlorides and the adjacent amino acids are also included because of the reported effect to promote PT.16 Finally, the QM/MM layer boundary is formed by cutting part of the outer-sphere amino residues. QM/MM computations are based on the two-layer electronic embedding ONIOM as implemented in Gaussian 09. For the QM layer, the UTPSSh functional was used with the basis set of LanL2DZ for Mn and Ca/Sr/K and 6-31G(d) for the rest of the elements in the QM layer. For the MM layer, the Amber MM force field was performed. The QM layer was fully relaxed, while the atoms except H and K were frozen in the MM layer. The models in this work are optimized in the high spin state in accordance with the S2 state (MnIII MnIV3) in the Kok cycle1,2 individually. Possible structures with the Mn valence as
Table 1. Relative Energy Differences (kcal/mol) for PSII S2 (III−IV−IV−IV) and (IV−IV−IV−III)a QM-high spin QM-low spina
S2 (III−IV−IV−IV)
S2 (IV−IV−IV−III)
0 0
6.926 8.224
The low spins for S2 (III IV IV IV) and S2 (IV IV IV III) are αββα and αααβ, respectively, according to Frank Neese’s work.46
a
III−IV−IV−IV structure in this work. In the OEC, one of the water bound to Mn1 (W2) has also been proposed as OH−.23 However, further investigation recorded in the Supporting Information (SI) shows that the conclusion in this work was not significantly changed, whether the W2 was H2O or OH−. The optimized S2 models with Ca2+, Sr2+, and K+ and without Ca2+ are denoted as S 2 −Ca, S 2−Sr, S 2 −K, and S 2−Ca-depleted, B
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Table 2. Important Distances (Å) between the Atoms Inside the OEC for S2−Ca, S2−Sr, S2−K, and S2−Ca-depleted distance
S2−Ca
S2−Sr
S2−K
S2−Ca-depleted
XRD3
XRD-Sr26
Mn1−Mn2 Mn2−Mn3 Mn3−Mn4 Mn1−Mn3 Mn1−M Mn2−M Mn3−M Mn4−M
2.75 2.76 2.72 3.27 3.53 3.38 3.52 3.82
2.74 2.77 2.73 3.29 3.59 3.49 3.60 3.84
2.73 2.76 2.72 3.26 3.64 3.58 3.69 3.83
2.73 2.75 2.70 3.25
2.84 2.89 2.97 3.29 3.51 3.36 3.41 3.79
2.81 2.94 2.86 3.34 3.55 3.55 3.63 4.01
(Ca/Sr) 2.7,2.8,3.3 2:1:1
(Ca)3.4,3.9 2:2/3:1 (Sr)3.5,4.0 2:2/3:1
occupies 61.7 and 68.7% of the HOMO distribution within the OEC for S2−Ca and S2−Sr, respectively. Considering the recent EPR study of PSII S3, which suggests that Mn1 is possibly oxidized into Mn(IV),29 S2−Ca and S2−Sr with the HOMOs dominated by Mn1 d orbitals can progress to the S3 state. By contrast, for S2−K and S2−Ca-depleted, the populations on O1, O3, O5, and Mn4 are all obviously increased compared with those for S2−Ca. In this case, the portion of the Mn1 dz2 orbital becomes 45.3 and 28.5% for S2−K and S2−Ca-depleted, lower than that for S2−Ca or S2−Sr. It is unfavorable for the S3 formation that the weight of the most possible oxidized atom (Mn1) in HOMO decreases. Comparing the topology of the HOMOs for the two groups, one can find that PSII with Ca2+ or Sr2+ seems to be more favorable for ET from Mn1 to Yz•. The decreased electron population in HOMOs for the inhibitory group may decrease the chance of oxidation of Mn1. The above discussion suggests that ET occurs from Mn1 to the already oxidized Yz• in S2. For the PT, it has been commonly recognized that the proton exit channel begins at Asp61 and terminates in a series of PsbO residues.20,30−33 Figure 4a−d shows schematically the optimized structures including Yz (Tyr161), His190, Asp61, the OEC, and the crystalline water molecules within them for the four models. (Details of the optimized structure are in the SI.) Before the oxidization of the OEC, Yz will lose an electron and a proton to afford Yz•. As shown schematically by the green arrows in Figure 4 a−d, His190, W4, and W5 could possibly accept the proton in all four models. According to the theory,34−36 PT is determined by the extent of vibrational overlap between the initial and final states. The vibrational coupling can be assumed to depend exponentially on the proton donor−acceptor distance; therefore, elongation of the proton donor−acceptor distance will significantly slow down the rate. Among the three candidates, His190 is more appropriate to be the proton acceptor because of the short donor−acceptor distance between Yz and His190. Actually, it has been widely recognized that there is PT back and forth between His190 and Yz during the redox reaction of Yz.37−39 Once the formation of Yz• occurs, the OEC is most likely to release a proton, and then, Mn1 can transfer an electron to the Yz• to continue the Kok cycle.21 The possible PT path has been denoted by the blue arrows in Figure 4a−d for S2−Ca, S2−Sr, S2−K, and S2−Ca-depleted, respectively. So far, it is generally recognized that O5 is possibly the slow exchange water that participated in the O−O formation.40,41 Therefore, the PT should have started from a water molecule close to O5 and connected to the H-bond network. One PT route has been proposed that PT starts from the new inserted water (Wex) bonding to Mn1 to the W1 based on a small model (Wex → W7 → W2 → W8 → W1).42 However, W8 and W7 are not that close to Wex or W1 considering all of the ambient amino acids.
respectively. According to the experimental results, the four models could be divided into two groups, an active group including PSII with Ca2+ and Sr2+ and an inhibitory group including PSII with K+ and without Ca2+. As shown in Table 2, both optimized PSII S2−Ca and S2−Sr structures are in good agreement with the reported EXAFs and XRD results.3,24−27 According to the reported EXAFs, the Mn−Mn distance, especially the 2.7 Å peak, was almost undisturbed by the Ca2+ depletion.11 Our calculation is in accordance with the conclusion. On the basis of the reasonable agreement of computational and experimental structures, we consider that PSII S2 structures in this work are accurate enough for discussion.
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EXAFs23−25
RESULTS AND DISCUSSION
Although it has been deduced that the substitution and the removal of Ca2+ do not influence the OEC structure, there are still slight geometry changes of the OEC influenced by the metal ions. The average Mn(IV)−O bond lengths are usually about 1.9 Å.28 As shown in Figure 2, judging from the bond lengths, except Mn1, all other Mn are in the valence of IV. The Mn4−O5 and Mn3−O5 bonds become shorter in the sequence of S2−Ca, S2−K, and S2−Ca-depleted, which might be caused by the charge decrease of the metal ions. The only Mn(III) is Mn1 in the OEC due to its five-coordinated structure. Besides the change in Mn(IV)−O bonds, it has been found that the Mn1−O5 distance and the γ angle along the Z-axis are also altered with the change of the metal ions. A recent mechanism proposed that an OH− might be bound to Mn1(IV) in S3, which has been supported by the EPR study for S3.29 To stabilize the new OH−, the Mn1−O5 distance should be as long as possible to make enough space for the OH−. By the same token, the γ angle along the Z-axis should be smaller than 180°, or else, the Mn1−OH− and O5−Mn4 bonds would be in a line, which is not reasonable or stable. As shown in Figure 2a, c, and d, the Mn1−O5 distance is decreased with the alternation of the metal ions, 3.01, 2.99, and 2.95 Å for S2−Ca, S2−K, and S2−Ca-depleted, respectively. On the other hand, the γ angle along the Z-axis is increased from 167 to 174° in the sequence of S2−Ca, S2−K, and S2−Ca-depleted. It could be deduced that it requires more geometrical variation to form the S3 state for the OEC with K+ substitution or Ca2+ removal. In order to study the S2−S3 transition involved in releasing a pair of an electron and a proton, we performed the analysis on the highest occupied molecular orbitals (HOMOs) of the four corresponding S2 models. In Figure 3, the HOMOs distributed within the OEC with the isosurface value of ±0.06 are shown for the four models, respectively. (HOMOs with isosurface threshold = ±0.01 are shown in the SI.) The orbital distribution is almost the same for S2−Ca and S2−Sr, except that the relative orbital population on O2 and O3 mutually switches. The main contributions of HOMOs are from the Mn1 dz2 orbital, which C
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Figure 2. OECs and metal−oxygen distances (Å) in S2−Ca (a), S2−Sr (b), S2−K (c), and S2−Ca-depleted (d).
S2−Sr model. On the other hand, the distances for the PTs are elongated, 2.76 (PT4), 2.79 (PT3), 2.69 (PT2), and 2.77 (PT1), along the path for S2−K. For S2−Ca-depleted, even longer proton donor−acceptor distances have been found for the PT2 and PT4. PT4 is most disturbed that the distances for the PT from W3 to W7 are calculated to be 2.69, 2.68, 2.76, and 3.04 Å for S2−Ca, S2−Sr, S2−K, and S2−Ca-depleted, respectively (Figure 4). These distances gradually elongating in OW3−OW7 suggest the increasing difficulty in PT. Notice that the experimental pKa of metal-aquo-ion or metal hydrolysis for Ca2+, Sr2+, and K+ is 12.80, 13.18, and 14.50, while the pKa of H2O is 15.7.44,45 The difference of the pKa value is beneficial for the PT from W3 to W7. When the Ca2+ is depleted, there is no pKa gradient to drive PT4. The longer proton donor−acceptor distances and the decreased pKa gradient caused by K+ substitution or Ca2+ depletion increase the difficulty in PT during S2−S3 transition. In addition to the geometry and pKa difference, the vibrations for the two groups are also significantly different. Part of the QM
W7 is not only H-bonded to W3, W2, and an outer water molecule (not shown in Figure 4) but is also bonded to the O C group of Asp170 with one of its hydrogens. Besides the Hbonds among water molecules, W8 is also attracted to the OC of Asn181. Because W8 and W7 are quite deviated from the described “water rocking” route, it would cost additional energy for the two waters relaxing to the right site to achieve the PT. Considering the existing water molecules, it is natural to infer that W3 is most likely involved in the PT because it is the water possibly coordinated to Mn143 or possibly taking part in the nucleophilic attack of O5 to form O2,41 and it links to Asp61 through the hydrogen-bonding network (Figure 4). As shown in Figure 4, current optimized structures suggest that the PT starts from W3 to W9 toward the proton exit channel via three hydrogenbonding water molecules (W3 → W7 → W2 → W8 → W9). The proton donor−acceptor distances along the path are 2.69 (PT4), 2.74 (PT3), 2.66 (PT2), and 2.78 (PT1) for S2−Ca. The path and the distance for each PT are almost the same in the D
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Figure 3. HOMO within the OEC (isosurface value = ±0.06) for S2−Ca (a), S2−Sr (b), S2−K (c), andS2−Ca-depleted (d).
Figure 4. Scheme of the PT process based on the optimized structures of Yz (Tyr161), His190, Asp61, OEC, and the hydrogen-bonding water molecules between them for S2−Ca (a), S2−Sr (b), S2−K (c), and S2−Ca-depleted (d). The oxygen atoms of the crystalline water are denoted by the name of the water. The solid lines represent the possible route, and the dashed lines represent the less possible route. The PT paths to Yz• are also shown by green arrows so that these paths are distinguishable from the water deprotonation.
For each case of S2−Ca, S2−Sr, and S2−K, there are three lowfrequency OH stretching modes induced by coupled vibrations among W9, W2, and W3, which indicates that the PT path might
structure has been abstracted to reduce the time cost for the vibrational analysis including the OEC, its surrounding seven ligands, W1−W9, Asp61, Tyr161, and His190 (see Figure S4, SI). E
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Table 3. Assignments of the Vibrational Modes Related to the PT for the Four Models S2−Ca
S2−Sr
frequency (intensity)a
assignment (vector)b
frequency (intensity)
3150 (882) 3233 (1083) 3313 (1265)
νW2Ha (+) νW9Ha (+) νW9Ha (+) νW2Ha (−) νW2Hb (−) νW3Ha (+)
3151 (919) 3234 (1065) 3330 (618)
S2−K
S2−Ca-depleted
assignment (vector)
frequency (intensity)
assignment (vector)
νW2Ha (+) νW9Ha (+) νW9Ha (+) νW2Ha (−) νW2Hb (−) νW3Ha (+)
3202 (854) 3271 (1276) 3398 (550)
νW9Ha (+) νW2Ha (+) νW2Ha (+) νW9Ha (−) νW2Hb (−) νW3Ha (+)
frequency (intensity)
assignment (vector)
3175 (2593) 3179 (529) 3390 (1174) 3596 (106)
νW9Ha (+) νW2Hb (−) νW2Hb (+) νW9Ha (+) νW2Ha (+) νW2Hb (−) νW3Ha (+) νW3Hb (+)
The frequency is calculated in cm−1, while the intensity calculated in kilometers per mole. bThe “+” and “−” are used to denote the displacement vector direction. The direction in which H moves close to the bound O is defined as “−”; the direction in which H move far away from the bound O is defined as “+”.
a
Figure 5. Illustration of the concerted vibrational modes and the corresponding frequencies (cm−1) for S2−Ca (a), S2−Sr (b), S2−K (c), and S2−Ca-depleted (d). The oxygen atoms of the crystalline water are denoted by the name of the water, while the two hydrogen atoms in the same water are distinguished as Ha and Hb. The vibration vectors for each frequency are denoted separately.
vibration combined with the weak W2−Ha (−) stretching vibration, as shown in Figure 5a. The mode at 3313 cm−1 is assigned to the W3−Ha stretching and the comparative W2−Hb (−) stretching. Each of the three modes involves at least two waters on the PT path with the preferred dissociative direction. Similar situations are also observed for S2−Sr and S2−K (in Figure 5b and c), except that the frequencies of the three
be as suggested from W3 to W9. The assignment of these bands is listed in Table 3, and the displacement vectors are shown in Figure 5a−c. (Details of all the normal modes beyond 3000 cm−1 can be found in the SI.) Take S2−Ca as an example; the strong W2−Ha stretching coupled with the weak W9−Ha stretching induces the vibration at 3150 cm−1, while the vibration of 3233 cm−1 is attributed to the strong W9−Ha stretching F
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We also acknowledge financial supporting of the Riken International Program Associate.
concerted vibrational modes for S2−K are much higher (3202, 3271, and 3398 cm−1) than that in S2−Ca. On the other hand, when Ca2+ is depleted, instead of concerted stretching modes, the W2−Ha and W3−Ha stretching vibrations are separately located at the modes dominated by its own asymmetric and symmetric stretching. As shown in Figure 5d and Table 3 (column 4), the vibrations at 3175 and 3179 cm−1 are mainly attributed to W9−Ha and W2−Hb instead of W2−Ha stretching modes. These two vibrations suggest that Hb of W2 is likely to be deprotonated while Ha of W9 is dissociated, which is totally different from that in S2−Ca. The high frequencies of the W2−Ha stretching (3390 cm−1) and the W3−Ha stretching (3596 cm−1) suggest apparent difficulty for PT (from W3 to W9) in S2−Ca-depleted. In line with the proton donor−acceptor distance, the PT in S2−K might be more difficult than that in S2−Ca due to three high-frequency-concerted vibrational bands. The PT in S2−Ca-depleted might be harder than S2−K due to the isolated OH stretching vibration and the higher OH stretching frequency of W2 and W3.
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(1) Kok, B.; Forbush, B.; McGloin, M. Cooperation of Charges in Photosynthetic O2 EvolutionI. A Linear Four Step Mechanism. J. Photochem. Photobiol. 1970, 11, 457−475. (2) Dau, H.; Haumann, M. The Manganese Complex of Photosystem II in Its Reaction CycleBasic Framework and Possible Realization at the Atomic Level. Coord. Chem. Rev. 2008, 252, 273−295. (3) Umena, Y.; Kawakami, K.; Shen, J. R.; Kamiya, N. Crystal Structure of Oxygen-Evolving Photosystem II at a Resolution of 1.9 A. Nature 2011, 473, 55−60. (4) Yano, J.; Yachandra, V. Mn4Ca Cluster in Photosynthesis: Where and How Water Is Oxidized to Dioxygen. Chem. Rev. 2014, 114, 4175− 4205. (5) Ghanotakis, D. F.; Babcock, G. T.; Yocum, C. F. Calcium Reconstitutes High Rates of Oxygen Evolution in Polypeptide Depleted Photosystem II Preparations. FEBS Lett. 1984, 167, 127−130. (6) Ghanotakis, D. F.; Topper, J. N.; Babcock, G. T.; Yocum, C. F. Water-Soluble 17 and 23 kDa Polypeptides Restore Oxygen Evolution Activity by Creating a High-Affinity Binding Site for Ca2+ on the Oxidizing Side of Photosystem II. FEBS Lett. 1984, 170, 169−173. (7) Ono, T.-a.; Inoue, Y. Discrete Extraction of the Ca Atom Functional for O2 Evolution in Higher Plant Photosystem II by a Simple Low pH Treatment. FEBS Lett. 1988, 227, 147−152. (8) Boussac, A.; Zimmermann, J.; Rutherford, A. EPR Signals from Modified Charge Accumulation States of the Oxygen Evolving Enzyme in Ca2+-Deficient Photosystem II. Biochemistry 1989, 28, 8984−8989. (9) Sivaraja, M.; Tso, J.; Dismukes, G. C.; Calcium-Specific Site, A. Influences the Structure and Activity of the Manganese Cluster Responsible for Photosynthetic Water Oxidation. Biochemistry 1989, 28, 9459−9464. (10) Tang, X.-S.; Randall, D. W.; Force, D. A.; Diner, B. A.; Britt, R. D. Manganese−Tyrosine Interaction in the Photosystem II OxygenEvolving Complex. J. Am. Chem. Soc. 1996, 118, 7638−7639. (11) Matthew, J. L.; Victoria, J. D.; Vittal, K. Y.; Kenneth, S.; Melvin, P. K. Structural Effects of Calcium Depletion on the Manganese Cluster of Photosystem II: Determination by X-ray Absorption Spectroscopy. J. Phys. Chem. B 1998, 102, 8257−8265. (12) Ono, T. A.; Inoue, Y. Roles of Ca2+ in O2 Evolution in Higher Plant Photosystem II: Effects of Replacement of Ca2+ Site by Other Cations. Arch. Biochem. Biophys. 1989, 275, 440−448. (13) Ono, T. A. Effects of Lanthanide Substitution at Ca2+-Site on the Properties of the Oxygen Evolving Center of Photosystem II. J. Inorg. Biochem. 2000, 82, 85−91. (14) Ono, T.-a.; Rompel, A.; Mino, H.; Chiba, N. Ca2+ Function in Photosynthetic Oxygen Evolution Studied by Alkali Metal Cations Substitution. Biophys. J. 2001, 81, 1831−1840. (15) Kimura, Y.; Hasegawa, K.; Ono, T.-a. Characteristic Changes of the S2/S1 Difference Ftir Spectrum Induced by Ca2+ Depletion and Metal Cation Substitution in the Photosynthetic Oxygen-Evolving Complex. Biochemistry 2002, 41, 5844−5853. (16) Yocum, C. The Calcium and Chloride Requirements of the O2 Evolving Complex. Coord. Chem. Rev. 2008, 252, 296−305. (17) Vrettos, J.; Stone, D.; Brudvig, G. Quantifying the Ion Selectivity of the Ca2+ Site in Photosystem II: Evidence for Direct Involvement of Ca2+ in O2 Formation. Biochemistry 2001, 40, 7937−7945. (18) Rappaport, F.; Ishida, N.; Sugiura, M.; Boussac, A. Ca2+ Determines the Entropy Changes Associated with the Formation of Transition States during Water Oxidation by Photosystem II. Energy Environ. Sci. 2011, 4, 2520−2524. (19) Polander, B. C.; Barry, B. A. Calcium and the Hydrogen-Bonded Water Network in the Photosynthetic Oxygen-Evolving Complex. J. Phys. Chem. Lett. 2013, 4, 786−791. (20) 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.
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CONCLUSION In the absence of Ca2+, W3 is considerably shifted, increasing the proton donor−acceptor distances. The decreased pKa gradient due to the depletion of Ca2+, the isolated OH stretching vibrations, and their high frequency also indicate that the PT toward the proton exit channel becomes much more difficult than that in natural PSII. The decreased electron population of the Mn1 dz2 orbital in the HOMO caused by the Ca2+ depletion also suggests the disadvantage of the ET initiated from Mn1. These four reasons might result in the situation that the Kok cycle stops at the S2 state with Yz oxidized. If K+ was added to compensate for the loss of Ca2+, all four disadvantageous factors would be slightly set back but still less favorable for the ET and PT than that for the natural PSII. These four issues might lead to the dramatic inhibition of the O2 activity, although the O2 activity is not 100% inhibitory. Only if Ca2+ or Sr2+ were added back to the system, the activity would restore effectively because of the recovery of the HOMOs and PT route. S2−Ca and S2−Sr have shared a lot in common in the S2 state; the reason for the decreased activity of Sr2+-substituted PSII might be found in S3 or later states. Ca2+ in PSII is the fundamental element adjusting the geometrical and electronic structure of the OEC and the surrounding water so as to facilitate the ET and PT.
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ASSOCIATED CONTENT
S Supporting Information *
Figures S1−S5, Tables S1 and S2, and the molecular coordination for all the optimized QM structures. This material is available free of charge via the Internet at http://pubs.acs.org.
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REFERENCES
AUTHOR INFORMATION
Corresponding Authors
*E-mail: [email protected]. Tel: 81-048-4679477 (S.N.). *E-mail: [email protected]. Tel: 86-411-84379070 (C.L.). Notes
The authors declare no competing financial interest.
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ACKNOWLEDGMENTS This work is financially supported by the National Science Foundation of China under Grant 21090340, 21361140346, the National Basic Research Program of China (2014CB239400). We used resources of the Riken Integrated Cluster of Clusters. G
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(21) Klauss, A.; Haumann, M.; Dau, H. Alternating Electron and Proton Transfer Steps in Photosynthetic Water Oxidation. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 16035−16040. (22) Polander, B. C.; Barry, B. A. Detection of an Intermediary, Protonated Water Cluster in Photosynthetic Oxygen Evolution. Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 10634−10639. (23) Ames, W.; Pantazis, D. A.; Krewald, V.; Cox, N.; Messinger, J.; Lubitz, W.; Neese, F. Theoretical Evaluation of Structural Models of the S2 State in the Oxygen Evolving Complex of Photosystem II: Protonation States and Magnetic Interactions. J. Am. Chem. Soc. 2011, 133, 19743−19757. (24) Yano, J.; et al. Where Water Is Oxidized to Dioxygen: Structure of the Photosynthetic Mn4Ca Cluster. Science 2006, 314, 821−825. (25) Dau, H.; Grundmeier, A.; Loja, P.; Haumann, M. On the Structure of the Manganese Complex of Photosystem II: Extended-Range Exafs Data and Specific Atomic-Resolution Models for Four S-States. Philos. Trans. R. Soc. London, Ser. B 2008, 363, 1237−1244. (26) Pushkar, Y.; Yano, J.; Sauer, K.; Boussac, A.; Yachandra, V. K. Structural Changes in the Mn4Ca Cluster and the Mechanism of Photosynthetic Water Splitting. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 1879−1884. (27) Koua, F. H.; Umena, Y.; Kawakami, K.; Shen, J. R. Structure of SrSubstituted Photosystem II at 2.1 Å Resolution and Its Implications in the Mechanism of Water Oxidation. Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 3889−3894. (28) Yamaguchi, K.; et al. The Nature of Chemical Bonds of the CaMn4O5 Cluster in Oxygen Evolving Complex of Photosystem II: Jahn−Teller Distortion and Its Suppression by Ca Doping in Cubane Structures. Int. J. Quantum Chem. 2013, 113, 453−473. (29) Cox, N.; Retegan, M.; Neese, F.; Pantazis, D. A.; Boussac, A.; Lubitz, W. Photosynthesis. Electronic Structure of the Oxygen-Evolving Complex in Photosystem II Prior to O−O Bond Formation. Science 2014, 345, 804−808. (30) Murray, J. W.; Barber, J. Structural Characteristics of Channels and Pathways in Photosystem II Including the Identification of an Oxygen Channel. J. Struct. Biol. 2007, 159, 228−237. (31) Ho, F. M.; Styring, S. Access Channels and Methanol Binding Site to the CaMn4 Cluster in Photosystem II Based on Solvent Accessibility Simulations, with Implications for Substrate Water Access. Biochim. Biophys. Acta, Bioenerg. 2008, 1777, 140−153. (32) Pal, R.; Negre, C.; Vogt, L.; Pokhrel, R.; Ertem, M.; Brudvig, G.; Batista, V. S0-State Model of the Oxygen-Evolving Complex of Photosystem II. Biochemistry 2013, 52, 7703−7706. (33) Shoji, M.; Isobe, H.; Yamanaka, S.; Umena, Y.; Kawakami, K.; Kamiya, N.; Shen, J. R.; Yamaguchi, K. Theoretical Insight in to Hydrogen-Bonding Networks and Proton Wire for the CaMn4O5 Cluster of Photosystem II. Elongation of Mn−Mn Distances with Hydrogen Bonds. Catal. Sci. Technol. 2013, 3, 1831−1848. (34) Layfield, J. P.; Hammes-Schiffer, S. Hydrogen Tunneling in Enzymes and Biomimetic Models. Chem. Rev. 2014, 114, 3466−3494. (35) Meyer, T. J.; Huynh, M. H. V.; Thorp, H. H. The Possible Role of Proton-Coupled Electron Transfer (PCET) in Water Oxidation by Photosystem II. Angew. Chem., Int. Ed. 2007, 46, 5284−5304. (36) Weinberg, D. R.; Gagliardi, C. J.; Hull, J. F.; Murphy, C. F.; Kent, C. A.; Westlake, B. C.; Paul, A.; Ess, D. H.; McCafferty, D. G.; Meyer, T. J. Proton-Coupled Electron Transfer. Chem. Rev. 2012, 112, 4016− 4093. (37) Barry, B. A. Proton Coupled Electron Transfer and Redox Active Tyrosines in Photosystem II. J. Photochem. Photobiol., B 2011, 104, 60− 71. (38) Gagliardi, C. J.; Vannucci, A. K.; Concepcion, J. J.; Chen, Z.; Meyer, T. J. The Role of Proton Coupled Electron Transfer in Water Oxidation. Energy Environ. Sci. 2012, 5, 7704−7717. (39) Hammarström, L.; Styring, S. Proton-Coupled Electron Transfer of Tyrosines in Photosystem II and Model Systems for Artificial Photosynthesis: The Role of a Redox-Active Link between Catalyst and Photosensitizer. Energy Environ. Sci. 2011, 4, 2379−2388.
(40) Siegbahn, P. E. Substrate Water Exchange for the Oxygen Evolving Complex in PSII in the S1, S2, and S3 States. J. Am. Chem. Soc. 2013, 135, 9442−9449. (41) Cox, N.; Pantazis, D. A.; Neese, F.; Lubitz, W. Biological Water Oxidation. Acc. Chem. Res. 2013, 46, 1588−1596. (42) Siegbahn, P. E. 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. (43) Siegbahn, P. E. M. Recent Theoretical Studies of Water Oxidation in Photosystem II. J. Photochem. Photobiol., B 2011, 104, 94−99. (44) Dean, J. A. Lange’s Handbook of Chemistry, 15 ed.; McGraw-Hill, Inc.: New York, 1985. (45) Baes, C. F.; Mesmer, R. E. The Hydrolysis of Cations; Wiley: New York, 1976. (46) Pantazis, D. A.; Ames, W.; Cox, N.; Lubitz, W.; Neese, F. Two Interconvertible Structures That Explain the Spectroscopic Properties of the Oxygen-Evolving Complex of Photosystem II in the S2 State. Angew. Chem., Int. Ed. 2012, 51, 9935−9940.
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dx.doi.org/10.1021/jp505889p | J. Phys. Chem. B XXXX, XXX, XXX−XXX
Theoretical Study on the Role of Ca2+ at the S2 State in Photosystem II Jingxiu Yang,† Makoto Hatakeyama,‡ Koji Ogata,‡ Shinichiro Nakamura,*,‡ and Can Li*,† †
State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, 116023 Dalian, People’s Republic of China ‡ Nakamura Laboratory, RIKEN Research Cluster for Innovation, 351-0198 Wako, Japan S Supporting Information *
ABSTRACT: In photosynthesis, calcium is crucial for oxygen evolution. In the absence of Ca2+, the Kok cycle has been proven to stop at S2 with Yz•. To explore the reason, photosystem II (PSII) S2 models (in total 32452 atoms) with different metal ions (Ca2+, Sr2+, and K+) or without Ca2+ involved in the oxygen evolution complex (OEC) have been theoretically studied based on the previous dynamic study of PSII. It is found that the portion of the Mn1 d-orbital decreases in the highest occupied molecular orbitals for Ca2+depleted PSII. This feature is unfavorable for the electron transfer from the OEC to the Yz•. Furthermore, the proton donor−acceptor distance was found elongated by the alternation of the binding water in the absence of Ca2+. The isolated vibrational modes of the key water molecules along the path and their high frequency of the OH stretching modes also suggested the difficulty of the proton transfer from the OEC toward the proton exit channel. This work provides one mechanistic explanation for the inactivity of Ca2+-depleted PSII.
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were all suggested able to replace Ca2+ yet were inhibitory for the oxygen evolution reaction in PSII.12−16 Except Ca2+, only Sr2+reconstructed PSII could recover about 50% steady activity.5,7,16 The reason for the mentioned change was once attributed to the different pKa of the metal ions, which acted as Lewis acids, binding the substrate water and tuning its reactivity.17 Besides, it has been recently deduced that Ca2+ rather than other metal ions maintains the correct configuration of the surrounding water network by pulsed EPR and FTIR spectroscopy.18,19 These findings all imply that the role of Ca2+ might relate to the electron transfer (ET) and proton transfer (PT) for the long-range oxidization in PSII. However, systematic investigation or further understanding of this issue is scarce. To explore the exact working mechanism of Ca2+, a Ca-depleted (inhibitory) S2 model and Ca2+ (active), Sr2+ (active), and K+ (inhibitory) substituted S2 models based on the previous dynamic study20 were optimized and analyzed by QM/MM method. We have found that Ca2+ or other substituted metal ions have influence on the geometrical and electronic structure of the OEC that is closely related to the ET and PT.
INTRODUCTION Nature’s light-driven water oxidization is performed by the oxygen evolving complex (OEC) of photosystem II (PSII). Water is decomposed into protons, electrons, and molecular oxygen while the OEC passes through five intermediate states of the so-called Kok cycle.1 Each electron release in the Kok cycle is initiated by the oxidation of tyrosine (Yz), which consequently oxidizes the OEC. The complex consists of an oxo-bridged Mn4 cluster containing primarily Mn(III) and Mn(IV) ions and one Ca2+ ion.2−4 This Ca2+ plays the crucial role in oxygen evolution; without Ca2+, the OEC could not achieve the S3 state. The study about the role of Ca2+ could go back to the 1980s.5−7 In 1984, Ghanotakis et al. found that high-salt-treated PSII produced 80% inhibition of O2 evolution.6 The addition of Ca2+ back to the salt-washed PSII can effectively recover the O2 evolution activity.6 Later, it was found that the inhibition could reach 91% in the absence of Ca2+, when the pH value was low enough.7 Boussac et al. and Sivaraja et al. reported the observation of a broad EPR signal centered at g = 2.0 for Ca-depleted samples at “S3”.8,9 Tang et al. proved that the “S3” EPR signal arose from the Yz• radical by pulsed ENDOR spectroscopy and ESEEM studies on citrate-treated PSII.10 Latimer and his coworkers reported that there was no evidence of Mn oxidization in the “S2−S3” transition for Ca-depleted PSII according to their Mn K-edge X-ray absorption spectroscopy study.11 In other words, illumination of Ca2+-depleted PSII allowed the S state to advance to an intermediate step where the CaMn4O5 cluster remained in the S2 state, yet Yz was oxidized and deprotonated to be a neutral Yz• radical. Other possible metal ion candidates to replace Ca2+ have been proposed and examined. Alkali metal, transition metal, and lanthanides ions such as K+, Cs+, Na+, Mn2+, Cd2+, and so forth © XXXX American Chemical Society
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COMPUTATIONAL MODELS AND METHOD The PSII model in this work is based on the recent X-ray crystal structure of PSII at 1.9 Å resolution,3 with 418 atoms in the QM layer and a total of 32452 atoms in the model. To obtain the well-optimized structure, a large QM layer was determined including the CaMn4O5, the directly coordinated first shell, part of the connected second-shell amino acids, and the crystal water Received: June 13, 2014 Revised: October 27, 2014
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Figure 1. Model of the QM layer for S2−Ca with different amino acids colored differently.
III−IV−IV−IV and IV−IV−IV−III were taken into account. Agreement had been reached that no proton release occurs during S1−S2 transition.2,4,21,22 Therefore, no proton release model has been adopted for S2. According to our calculation, the III−IV−IV−IV structure turned out to be energetically more stable than the IV−IV−IV−III structure by 6.92 kcal mol−1 shown in Table 1. Thus, we focus on the analysis of the S2
molecules within the structure. As shown in Figure 1, different amino acids are colored separately. Besides the OEC, our models contain the seven directly coordinated amino acids (all from chain D1, unless otherwise indicated) such as Asp170, Glu189, His332, Glu333, Asp342, Ala344, and CP43-Glu354. In addition, the Asp61, His337, and CP43-Arg357 are also included because they form hydrogen bonds with several oxygen atoms in the OEC. Certainly, the models contain His190, Tyr161 (Yz), and the hydrogen-bonded water molecules because of the H-bond network surrounding the OEC. Moreover, the two chlorides and the adjacent amino acids are also included because of the reported effect to promote PT.16 Finally, the QM/MM layer boundary is formed by cutting part of the outer-sphere amino residues. QM/MM computations are based on the two-layer electronic embedding ONIOM as implemented in Gaussian 09. For the QM layer, the UTPSSh functional was used with the basis set of LanL2DZ for Mn and Ca/Sr/K and 6-31G(d) for the rest of the elements in the QM layer. For the MM layer, the Amber MM force field was performed. The QM layer was fully relaxed, while the atoms except H and K were frozen in the MM layer. The models in this work are optimized in the high spin state in accordance with the S2 state (MnIII MnIV3) in the Kok cycle1,2 individually. Possible structures with the Mn valence as
Table 1. Relative Energy Differences (kcal/mol) for PSII S2 (III−IV−IV−IV) and (IV−IV−IV−III)a QM-high spin QM-low spina
S2 (III−IV−IV−IV)
S2 (IV−IV−IV−III)
0 0
6.926 8.224
The low spins for S2 (III IV IV IV) and S2 (IV IV IV III) are αββα and αααβ, respectively, according to Frank Neese’s work.46
a
III−IV−IV−IV structure in this work. In the OEC, one of the water bound to Mn1 (W2) has also been proposed as OH−.23 However, further investigation recorded in the Supporting Information (SI) shows that the conclusion in this work was not significantly changed, whether the W2 was H2O or OH−. The optimized S2 models with Ca2+, Sr2+, and K+ and without Ca2+ are denoted as S 2 −Ca, S 2−Sr, S 2 −K, and S 2−Ca-depleted, B
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Table 2. Important Distances (Å) between the Atoms Inside the OEC for S2−Ca, S2−Sr, S2−K, and S2−Ca-depleted distance
S2−Ca
S2−Sr
S2−K
S2−Ca-depleted
XRD3
XRD-Sr26
Mn1−Mn2 Mn2−Mn3 Mn3−Mn4 Mn1−Mn3 Mn1−M Mn2−M Mn3−M Mn4−M
2.75 2.76 2.72 3.27 3.53 3.38 3.52 3.82
2.74 2.77 2.73 3.29 3.59 3.49 3.60 3.84
2.73 2.76 2.72 3.26 3.64 3.58 3.69 3.83
2.73 2.75 2.70 3.25
2.84 2.89 2.97 3.29 3.51 3.36 3.41 3.79
2.81 2.94 2.86 3.34 3.55 3.55 3.63 4.01
(Ca/Sr) 2.7,2.8,3.3 2:1:1
(Ca)3.4,3.9 2:2/3:1 (Sr)3.5,4.0 2:2/3:1
occupies 61.7 and 68.7% of the HOMO distribution within the OEC for S2−Ca and S2−Sr, respectively. Considering the recent EPR study of PSII S3, which suggests that Mn1 is possibly oxidized into Mn(IV),29 S2−Ca and S2−Sr with the HOMOs dominated by Mn1 d orbitals can progress to the S3 state. By contrast, for S2−K and S2−Ca-depleted, the populations on O1, O3, O5, and Mn4 are all obviously increased compared with those for S2−Ca. In this case, the portion of the Mn1 dz2 orbital becomes 45.3 and 28.5% for S2−K and S2−Ca-depleted, lower than that for S2−Ca or S2−Sr. It is unfavorable for the S3 formation that the weight of the most possible oxidized atom (Mn1) in HOMO decreases. Comparing the topology of the HOMOs for the two groups, one can find that PSII with Ca2+ or Sr2+ seems to be more favorable for ET from Mn1 to Yz•. The decreased electron population in HOMOs for the inhibitory group may decrease the chance of oxidation of Mn1. The above discussion suggests that ET occurs from Mn1 to the already oxidized Yz• in S2. For the PT, it has been commonly recognized that the proton exit channel begins at Asp61 and terminates in a series of PsbO residues.20,30−33 Figure 4a−d shows schematically the optimized structures including Yz (Tyr161), His190, Asp61, the OEC, and the crystalline water molecules within them for the four models. (Details of the optimized structure are in the SI.) Before the oxidization of the OEC, Yz will lose an electron and a proton to afford Yz•. As shown schematically by the green arrows in Figure 4 a−d, His190, W4, and W5 could possibly accept the proton in all four models. According to the theory,34−36 PT is determined by the extent of vibrational overlap between the initial and final states. The vibrational coupling can be assumed to depend exponentially on the proton donor−acceptor distance; therefore, elongation of the proton donor−acceptor distance will significantly slow down the rate. Among the three candidates, His190 is more appropriate to be the proton acceptor because of the short donor−acceptor distance between Yz and His190. Actually, it has been widely recognized that there is PT back and forth between His190 and Yz during the redox reaction of Yz.37−39 Once the formation of Yz• occurs, the OEC is most likely to release a proton, and then, Mn1 can transfer an electron to the Yz• to continue the Kok cycle.21 The possible PT path has been denoted by the blue arrows in Figure 4a−d for S2−Ca, S2−Sr, S2−K, and S2−Ca-depleted, respectively. So far, it is generally recognized that O5 is possibly the slow exchange water that participated in the O−O formation.40,41 Therefore, the PT should have started from a water molecule close to O5 and connected to the H-bond network. One PT route has been proposed that PT starts from the new inserted water (Wex) bonding to Mn1 to the W1 based on a small model (Wex → W7 → W2 → W8 → W1).42 However, W8 and W7 are not that close to Wex or W1 considering all of the ambient amino acids.
respectively. According to the experimental results, the four models could be divided into two groups, an active group including PSII with Ca2+ and Sr2+ and an inhibitory group including PSII with K+ and without Ca2+. As shown in Table 2, both optimized PSII S2−Ca and S2−Sr structures are in good agreement with the reported EXAFs and XRD results.3,24−27 According to the reported EXAFs, the Mn−Mn distance, especially the 2.7 Å peak, was almost undisturbed by the Ca2+ depletion.11 Our calculation is in accordance with the conclusion. On the basis of the reasonable agreement of computational and experimental structures, we consider that PSII S2 structures in this work are accurate enough for discussion.
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EXAFs23−25
RESULTS AND DISCUSSION
Although it has been deduced that the substitution and the removal of Ca2+ do not influence the OEC structure, there are still slight geometry changes of the OEC influenced by the metal ions. The average Mn(IV)−O bond lengths are usually about 1.9 Å.28 As shown in Figure 2, judging from the bond lengths, except Mn1, all other Mn are in the valence of IV. The Mn4−O5 and Mn3−O5 bonds become shorter in the sequence of S2−Ca, S2−K, and S2−Ca-depleted, which might be caused by the charge decrease of the metal ions. The only Mn(III) is Mn1 in the OEC due to its five-coordinated structure. Besides the change in Mn(IV)−O bonds, it has been found that the Mn1−O5 distance and the γ angle along the Z-axis are also altered with the change of the metal ions. A recent mechanism proposed that an OH− might be bound to Mn1(IV) in S3, which has been supported by the EPR study for S3.29 To stabilize the new OH−, the Mn1−O5 distance should be as long as possible to make enough space for the OH−. By the same token, the γ angle along the Z-axis should be smaller than 180°, or else, the Mn1−OH− and O5−Mn4 bonds would be in a line, which is not reasonable or stable. As shown in Figure 2a, c, and d, the Mn1−O5 distance is decreased with the alternation of the metal ions, 3.01, 2.99, and 2.95 Å for S2−Ca, S2−K, and S2−Ca-depleted, respectively. On the other hand, the γ angle along the Z-axis is increased from 167 to 174° in the sequence of S2−Ca, S2−K, and S2−Ca-depleted. It could be deduced that it requires more geometrical variation to form the S3 state for the OEC with K+ substitution or Ca2+ removal. In order to study the S2−S3 transition involved in releasing a pair of an electron and a proton, we performed the analysis on the highest occupied molecular orbitals (HOMOs) of the four corresponding S2 models. In Figure 3, the HOMOs distributed within the OEC with the isosurface value of ±0.06 are shown for the four models, respectively. (HOMOs with isosurface threshold = ±0.01 are shown in the SI.) The orbital distribution is almost the same for S2−Ca and S2−Sr, except that the relative orbital population on O2 and O3 mutually switches. The main contributions of HOMOs are from the Mn1 dz2 orbital, which C
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Figure 2. OECs and metal−oxygen distances (Å) in S2−Ca (a), S2−Sr (b), S2−K (c), and S2−Ca-depleted (d).
S2−Sr model. On the other hand, the distances for the PTs are elongated, 2.76 (PT4), 2.79 (PT3), 2.69 (PT2), and 2.77 (PT1), along the path for S2−K. For S2−Ca-depleted, even longer proton donor−acceptor distances have been found for the PT2 and PT4. PT4 is most disturbed that the distances for the PT from W3 to W7 are calculated to be 2.69, 2.68, 2.76, and 3.04 Å for S2−Ca, S2−Sr, S2−K, and S2−Ca-depleted, respectively (Figure 4). These distances gradually elongating in OW3−OW7 suggest the increasing difficulty in PT. Notice that the experimental pKa of metal-aquo-ion or metal hydrolysis for Ca2+, Sr2+, and K+ is 12.80, 13.18, and 14.50, while the pKa of H2O is 15.7.44,45 The difference of the pKa value is beneficial for the PT from W3 to W7. When the Ca2+ is depleted, there is no pKa gradient to drive PT4. The longer proton donor−acceptor distances and the decreased pKa gradient caused by K+ substitution or Ca2+ depletion increase the difficulty in PT during S2−S3 transition. In addition to the geometry and pKa difference, the vibrations for the two groups are also significantly different. Part of the QM
W7 is not only H-bonded to W3, W2, and an outer water molecule (not shown in Figure 4) but is also bonded to the O C group of Asp170 with one of its hydrogens. Besides the Hbonds among water molecules, W8 is also attracted to the OC of Asn181. Because W8 and W7 are quite deviated from the described “water rocking” route, it would cost additional energy for the two waters relaxing to the right site to achieve the PT. Considering the existing water molecules, it is natural to infer that W3 is most likely involved in the PT because it is the water possibly coordinated to Mn143 or possibly taking part in the nucleophilic attack of O5 to form O2,41 and it links to Asp61 through the hydrogen-bonding network (Figure 4). As shown in Figure 4, current optimized structures suggest that the PT starts from W3 to W9 toward the proton exit channel via three hydrogenbonding water molecules (W3 → W7 → W2 → W8 → W9). The proton donor−acceptor distances along the path are 2.69 (PT4), 2.74 (PT3), 2.66 (PT2), and 2.78 (PT1) for S2−Ca. The path and the distance for each PT are almost the same in the D
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Figure 3. HOMO within the OEC (isosurface value = ±0.06) for S2−Ca (a), S2−Sr (b), S2−K (c), andS2−Ca-depleted (d).
Figure 4. Scheme of the PT process based on the optimized structures of Yz (Tyr161), His190, Asp61, OEC, and the hydrogen-bonding water molecules between them for S2−Ca (a), S2−Sr (b), S2−K (c), and S2−Ca-depleted (d). The oxygen atoms of the crystalline water are denoted by the name of the water. The solid lines represent the possible route, and the dashed lines represent the less possible route. The PT paths to Yz• are also shown by green arrows so that these paths are distinguishable from the water deprotonation.
For each case of S2−Ca, S2−Sr, and S2−K, there are three lowfrequency OH stretching modes induced by coupled vibrations among W9, W2, and W3, which indicates that the PT path might
structure has been abstracted to reduce the time cost for the vibrational analysis including the OEC, its surrounding seven ligands, W1−W9, Asp61, Tyr161, and His190 (see Figure S4, SI). E
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Table 3. Assignments of the Vibrational Modes Related to the PT for the Four Models S2−Ca
S2−Sr
frequency (intensity)a
assignment (vector)b
frequency (intensity)
3150 (882) 3233 (1083) 3313 (1265)
νW2Ha (+) νW9Ha (+) νW9Ha (+) νW2Ha (−) νW2Hb (−) νW3Ha (+)
3151 (919) 3234 (1065) 3330 (618)
S2−K
S2−Ca-depleted
assignment (vector)
frequency (intensity)
assignment (vector)
νW2Ha (+) νW9Ha (+) νW9Ha (+) νW2Ha (−) νW2Hb (−) νW3Ha (+)
3202 (854) 3271 (1276) 3398 (550)
νW9Ha (+) νW2Ha (+) νW2Ha (+) νW9Ha (−) νW2Hb (−) νW3Ha (+)
frequency (intensity)
assignment (vector)
3175 (2593) 3179 (529) 3390 (1174) 3596 (106)
νW9Ha (+) νW2Hb (−) νW2Hb (+) νW9Ha (+) νW2Ha (+) νW2Hb (−) νW3Ha (+) νW3Hb (+)
The frequency is calculated in cm−1, while the intensity calculated in kilometers per mole. bThe “+” and “−” are used to denote the displacement vector direction. The direction in which H moves close to the bound O is defined as “−”; the direction in which H move far away from the bound O is defined as “+”.
a
Figure 5. Illustration of the concerted vibrational modes and the corresponding frequencies (cm−1) for S2−Ca (a), S2−Sr (b), S2−K (c), and S2−Ca-depleted (d). The oxygen atoms of the crystalline water are denoted by the name of the water, while the two hydrogen atoms in the same water are distinguished as Ha and Hb. The vibration vectors for each frequency are denoted separately.
vibration combined with the weak W2−Ha (−) stretching vibration, as shown in Figure 5a. The mode at 3313 cm−1 is assigned to the W3−Ha stretching and the comparative W2−Hb (−) stretching. Each of the three modes involves at least two waters on the PT path with the preferred dissociative direction. Similar situations are also observed for S2−Sr and S2−K (in Figure 5b and c), except that the frequencies of the three
be as suggested from W3 to W9. The assignment of these bands is listed in Table 3, and the displacement vectors are shown in Figure 5a−c. (Details of all the normal modes beyond 3000 cm−1 can be found in the SI.) Take S2−Ca as an example; the strong W2−Ha stretching coupled with the weak W9−Ha stretching induces the vibration at 3150 cm−1, while the vibration of 3233 cm−1 is attributed to the strong W9−Ha stretching F
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We also acknowledge financial supporting of the Riken International Program Associate.
concerted vibrational modes for S2−K are much higher (3202, 3271, and 3398 cm−1) than that in S2−Ca. On the other hand, when Ca2+ is depleted, instead of concerted stretching modes, the W2−Ha and W3−Ha stretching vibrations are separately located at the modes dominated by its own asymmetric and symmetric stretching. As shown in Figure 5d and Table 3 (column 4), the vibrations at 3175 and 3179 cm−1 are mainly attributed to W9−Ha and W2−Hb instead of W2−Ha stretching modes. These two vibrations suggest that Hb of W2 is likely to be deprotonated while Ha of W9 is dissociated, which is totally different from that in S2−Ca. The high frequencies of the W2−Ha stretching (3390 cm−1) and the W3−Ha stretching (3596 cm−1) suggest apparent difficulty for PT (from W3 to W9) in S2−Ca-depleted. In line with the proton donor−acceptor distance, the PT in S2−K might be more difficult than that in S2−Ca due to three high-frequency-concerted vibrational bands. The PT in S2−Ca-depleted might be harder than S2−K due to the isolated OH stretching vibration and the higher OH stretching frequency of W2 and W3.
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CONCLUSION In the absence of Ca2+, W3 is considerably shifted, increasing the proton donor−acceptor distances. The decreased pKa gradient due to the depletion of Ca2+, the isolated OH stretching vibrations, and their high frequency also indicate that the PT toward the proton exit channel becomes much more difficult than that in natural PSII. The decreased electron population of the Mn1 dz2 orbital in the HOMO caused by the Ca2+ depletion also suggests the disadvantage of the ET initiated from Mn1. These four reasons might result in the situation that the Kok cycle stops at the S2 state with Yz oxidized. If K+ was added to compensate for the loss of Ca2+, all four disadvantageous factors would be slightly set back but still less favorable for the ET and PT than that for the natural PSII. These four issues might lead to the dramatic inhibition of the O2 activity, although the O2 activity is not 100% inhibitory. Only if Ca2+ or Sr2+ were added back to the system, the activity would restore effectively because of the recovery of the HOMOs and PT route. S2−Ca and S2−Sr have shared a lot in common in the S2 state; the reason for the decreased activity of Sr2+-substituted PSII might be found in S3 or later states. Ca2+ in PSII is the fundamental element adjusting the geometrical and electronic structure of the OEC and the surrounding water so as to facilitate the ET and PT.
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ASSOCIATED CONTENT
S Supporting Information *
Figures S1−S5, Tables S1 and S2, and the molecular coordination for all the optimized QM structures. This material is available free of charge via the Internet at http://pubs.acs.org.
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REFERENCES
AUTHOR INFORMATION
Corresponding Authors
*E-mail: [email protected]. Tel: 81-048-4679477 (S.N.). *E-mail: [email protected]. Tel: 86-411-84379070 (C.L.). Notes
The authors declare no competing financial interest.
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ACKNOWLEDGMENTS This work is financially supported by the National Science Foundation of China under Grant 21090340, 21361140346, the National Basic Research Program of China (2014CB239400). We used resources of the Riken Integrated Cluster of Clusters. G
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