of a Proton-Conducting Water Chain in ... - ACS Publications

Perspective pubs.acs.org/JPCL

pKa of a Proton-Conducting Water Chain in Photosystem II Tomohiro Takaoka,† Naoki Sakashita,† Keisuke Saito,†,‡,§ and Hiroshi Ishikita*,†,‡ †

Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan § Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan ‡

S Supporting Information *

ABSTRACT: Recent high-resolution crystal structures of the water-oxidizing enzyme photosystem II (PSII) show that O4 of the catalytic Mn4CaO5 cluster forms an H-bond with a water molecule W539, which belongs to a chain of water molecules (O4-water chain). Oxidation of Mn4CaO5 to S1 resulted in elongation of the O−H bonds and decrease in pKa(O−H/O−) in the [O4−H···OW539−H···OW538−H···OW393] region along the O4-water chain. In S1, removal of all water molecules from the O4-water chain, except W539, resulted in a significant pKa upshift at O4; this suggests that the protonconducting water chain serves as a conducting media for protons and significantly decreases the donor pKa, leading to a downhill proton transfer. The absence of a corresponding proton-conducting channel is disadvantageous for release of protons from the proton-releasing site, as in the case of O5 that has no H-bond partner.

I

mechanics/molecular mechanics (QM/MM) studies by Pal et al. demonstrated that OH− at O5 has no direct-H-bond partner in the PSII protein environment;19 this implies that the “energy barrier” for proton transfer with O5 must be significantly high. The presence of a conserved hydrophobic amino acid side chain, D1-Val185, which is crucial for O2 production,21 does not form a stable H-bond with OH− at O5. It seems possible that without rotating the Mn-ligated D1-His332 side-chain by ∼90° and removing the D1-Val185 side-chain, a water molecule could not be placed at the position required for it to accept an H-bond from O5.7,20 On the other hand, both the 1.9 Å17 and free electron laser18 structures show the presence of a chain of 8 or 9 H-bonded water molecules (O4-water chain, summarized in ref 7) directly linked to O4 (linking Mn4 and Mn3 in the Mn3CaO4-cubane) (Figure 1b). Recent QM/MM studies demonstrated that the O4 water chain can function as a proton-conducting channel from hydroxyl O4 toward the PSII bulk surface.7 The potential energy profile indicates that along the O4-water chain the uphill proton-transfer reaction occurs in S0, where [(Mn1, Mn2, Mn3, Mn4) = (III, IV, III, III)], but the downhill protontransfer reaction in S1, where [(Mn1, Mn2, Mn3, Mn4) = (III, IV, IV, III)].7 These should contribute to a smaller activation energy for deprotonation, a property consistent with the known characteristics of the S0−S1 transition, which

n photosystem II (PSII), the Mn4CaO5 cluster catalyzes the water-splitting reaction: 2H2O → O2 + 4H+ + 4e−. The release of protons has been observed in response to changes in the oxidation state (the Sn state, where the subscript represents the number of oxidation steps accumulated) of the oxygenevolving complex and occurs with a typical stoichiometry of 1:0:1:2 for the S0 → S1 → S2 → S3 → S0 transitions, respectively. Candidates for the relevant proton-transfer pathways (e.g., see refs 1−6) and the proton-releasing sites (e.g., see ref 7) have been reviewed recently. The energetically lowest process for proton release from the Mn4CaO5 cluster is the S0−S1 transition, where the electron-transfer step occurs prior to H+ release and is thus rate-limiting.23 It has been argued that the exchangeable μ-oxo bridge is possibly either O4 (linking Mn4 and Mn3 in the Mn3CaO4-cubane) or O5 (in one of the corners of the cubane linking Mn4 and the cubane)8−11 (see also relevant articles published prior to the detailed crystal structure12−14), and some experimental observations favor O5 over O4 as the exchangeable bridge and the potential substrate8,9,11,15 (Figure 1a). Nevertheless, O4 was not ruled out in relevant experimental studies (e.g., EPR8). It should also be noted that a synthetic Mn4Ca cluster reported by Zhang et al. has four Mn atoms and four O atoms that correspond to all Mn and O atoms of the Mn4CaO5 cluster in PSII except O4;16 this could possibly suggest that O5 is a structural prerequisite, whereas O4 is removable or exchangeable. O5 has no direct H-bond partner in the 1.9 Å structure17 and in the free electron laser structure18 (Figure 1). Although some studies have suggested or assumed that O5 (= OH−) deprotonation occurs on the S0−S1 transition,9,19,20 recent quantum © XXXX American Chemical Society

Received: March 23, 2016 Accepted: April 29, 2016

1925

DOI: 10.1021/acs.jpclett.6b00656 J. Phys. Chem. Lett. 2016, 7, 1925−1932

The Journal of Physical Chemistry Letters

Perspective

We present the pKa values of all O−H sites of the water molecules in the O4-water chain to elucidate the mechanisms of the proton transfer mediated by the proton-conducting water chain. free-energy difference of [AH] and [A−] in water (ΔGwater), using the following equations: pK a = ΔGwater /2.303RT

(1)

ΔGwater = ΔGgas + ΔGsolv (A−) + ΔGsolv (H+) − ΔGsolv (AH) (2)

where R is the gas constant, T the temperature, ΔGgas the gasphase free-energy difference of [AH] and [A−], and ΔGsolv the free energy of solvation (thermodynamic-cycle approach). The thermodynamic-cycle approach, however, has the following uncertainties: (i) The proton solvation energy ΔGsolv(H+) is ambiguous, ranging from −252.6 to −271.7 kcal/mol (summarized in ref 30); (ii) The choice of the atomic radii can easily affect ΔGsolv(A−) for acids or ΔGsolv(AH) for bases. Although the thermodynamic approach has already been used for pKa calculations of Mn(H2O)631 or Mn4CaO5 in PSII,32 different parameter sets were used for these similar systems (see also the concluding remark in ref 32 for the uncertainty of the results). It has been demonstrated that the shapes of the H-bond potential-energy curves are predominantly determined by the pKa difference between the donor and acceptor moieties. Accordingly, H-bonds can be classified into single-well, lowbarrier, and standard (asymmetric double-well) H-bonds.25,26,29 Single-well H bonds have larger 1H NMR chemical shifts (δH) than standard H-bonds.33 Thus, δH of H-bonds should be correlated with the pKa values of the titratable groups34 in the presence of the same H-bond acceptor (or donor) atom. Notably, quantum chemical calculations (including QM/MM) can effectively reproduce experimentally measured δH for [Odonor−H···Oacceptor] bonds (e.g., see refs 34 and 35), because δH is predominantly determined by the local [Odonor−H··· Oacceptor] geometry (see also ref 36 for the empirical equations of δH and [Odonor−H···Oacceptor] lengths). Figure 2 shows that experimentally measured pKa(O−H/O−) of 36 titratable molecules (listed in Table S1) and calculated δH (B3LYP/ LACVP**) of [Odonor−H···Oacceptor] bonds are correlated (R2 = 0.97). The correlation shown in Figure 2 could be fitted to the following equation:

Figure 1. Overview of the catalytic site of PSII: (a) the Mn4CaO5 cluster and (b) the O4-water chain and the O5 path.

includes its rate being insensitive to H2O/D2O exchange and its activation energy being lower than that of the S2−S3 transition.22−24 In the 1.9 Å structure,17 W539 is the H-bond partner of O4. The O4−OW539 length is 2.43−2.50 Å,17 significantly shorter than typical O−O distances of ∼2.8 Å for H2O.39,40 In S0 [(Mn1, Mn2, Mn3, Mn4) = (III, IV, III, III)], the energy profile of the O4−H···OW539 bond resembles a standard (asymmetric double-well) H-bond, which describes an uphill proton transfer from O4−H···OW539. In contrast, when S1 [(Mn1, Mn2, Mn3, Mn4) = (III, IV, IV, III)] was formed, the energy profile of the O4−H···OW539 bond resembled a single-well H-bond, which essentially describes a barrierless proton transfer from O4−H···OW539.7 Single-well H-bonds, including low-barrier hydrogen bonds, can be formed only when the pKa difference between donor and acceptor moieties is nearly zero (matching pKa).25−29 These results indicate that matching of the pKa values of the donor (i.e., O4) and acceptor (i.e., W539 in the O4-water chain) moieties occurs in S1. Obviously, the local proton transfer within the single-well O4−H···OW539 bond is the trigger of the long-distance proton transfer along the entire water chain over a distance of 13.5 Å.7 The proton-conducting O4-water chain, one of the longest H-bonded straight water chains identified in protein crystal structures, is worthy of study in its own right. Here, we present the pKa values of all O−H sites of the water molecules in the O4-water chain to elucidate the mechanisms of the proton transfer mediated by the proton-conducting water chain. Obtaining pKa from 1H NMR Chemical Shifts: The “pKa-fromδH” Approach. pKa(AH/A−) for a titratable group A (AH, protonated and A−, unprotonated) can be calculated from the

pK a(O−H/O−) = −1.53δ H + 21.4

(3)

where Odonor−H is the titratable site and Oacceptor is an H2O molecule, the simplest and most relevant O−H···O bonds (Figure 2). It is possible that pKa(O−H/O−) can be reproduced using quantum-chemically optimized local [Otitratable−H···OH2] geometry. This also holds true for the case using QM/MM geometry of proteins, as demonstrated in ref 34. Equation 3 indicates that the elongation of the Odonor−H bond toward the acceptor water molecule, which corresponds to an increase in δH, results in a decrease in pKa(O−H/O−). The pKa-from-δH approach presented here avoids calculating the crucial terms, the gas-phase and solvation energy of the titratable molecule (in the protonated and unprotonated states) 1926



Perspective

The pKa-from-δH approach is directly applicable to the O−H site ligated to Mn using the quantum chemically optimized geometry; this is obvious from the fact that in the protein environment of PSII, the shape of the H-bond potential is also highly associated with δH of the Mn4CaO5 moiety. 2.55 Å in S0 is also shorter than typical O−O distances of ∼2.8 Å for H2O, but δH is small at 9.4 ppm, which is a typical value for standard H-bonds, Table 1). Using eq 3, pKa(O4−H/O4−) is 7.1 in S0 and −1.5 in S1 (Table 1, Figure 3a,b): the significant decrease in pKa(O4−H/O4−) in the S0−S1 transition should provide the driving force for the release of the proton from O4 toward the acceptor W539. It should be noted that once O4 releases the proton, the proton moves to the initial acceptor side (e.g., W539), which alters pKa in the entire proton-transfer pathway, most significantly at the second acceptor side (e.g., W538); thus, as the proton moves, alteration in pKa propagates along the proton-transfer pathway and the pKa values in the O4-water chain will be updated accordingly (see also Figure 3c for pKa values after proton transfer occurs, i.e., H+ at W399 in the “post-PT” H-bond pattern). Mechanism of Proton Transfer along the O4-Water Channel. Stuchebrukhov classified mechanisms of proton transfer in proteins as follows:38 Case 1: “localized charge transfer” model; there are insufficient water molecules in the channel, as suggested for cytochrome c oxidase.37 The proton transfer is characterized as a movement of the charged water ions, H3O+ or OH−. Case 2: “thermally activated hopping random walk” model; water molecules are weakly or partially H-bonded in the water chain. The random walk along the water chain is governed by the redox state of the enzyme. Case 3: “delocalized soliton transfer” model; all water molecules are strongly H-bonded in the water chain. The length of the water chain is realistically in the range of only 3−5 water molecules in proteins; the charge is delocalized along the entire water chain; the activation energy of the proton transfer is the lowest in the three cases.38

Figure 2. Correlation of the experimentally measured pKa(O−H/O−) of 36 titratable molecules (Table S1) and calculated δH in ppm for the [Odonor−H···Oacceptor] bonds, where Oacceptor is H2O/H3O+ (e.g., Odonor−H···OacceptorH2/Odonor−···H3Oacceptor+). δH was calculated using the GIAOs method49 implemented in the Jaguar51 program with the unrestricted DFT method with the B3LYP functional and LACVP** basis sets. R2 = 0.97.

required for the thermodynamic-cycle approach, but focuses only on δH of the O−H···O bond that is highly associated with the potential energy profile,29,34 because pKa of a titratable site is sufficiently represented at the local O−H site, as demonstrated in Figure 2. The pKa-from-δH approach is directly applicable to the O−H site ligated to Mn using the quantum chemically optimized geometry; this is obvious from the fact that in the protein environment of PSII, the shape of the H-bond potential is also highly associated with δH of the Mn4CaO5 moiety, e.g., (i) the potential energy profile of the single-well O4−OW539 in S1 resembles that of the typical single-well H-bond, which indicates that matching the pKa values of the donor and acceptor moieties occurs;7 (ii) δH for O4−OW539 is significantly large in S1 (Table 1, see discussion below). pKa(O4−H/O4−) in S0 and S1. Figure 3a shows pKa values of the proton-transfer pathway before proton transfer occurs, i.e., H+ at O4 in the “pre-PT” H-bond pattern. In the 1.9 Å structure,17 the O4−OW539 bond is significantly short, 2.43−2.50 Å. QM/MM calculations resulted in 2.55 Å in S0 for the O4−OW539 bond.7 In S1, the O4−OW539 bond is significantly shortened to 2.45 Å and the O4−H bond is significantly elongated toward the acceptor OW539 moiety, which results in δH = 15.0 ppm (Table 1). (Note that the O4−OW539 bond of Table 1. Calculated δH (ppm) and pKaa

without O4-water chainb

with O4-water chain δH O4−HO4 OW539−HW539 OW538−HW538 OW393−HW393 OW397−HW397 OW477−HW477 OW545−HW545 OW1047−HW1047

δH

pKa

pKa

S0

S1

S0

S1

S0

S1

S0

S1

9.4 9.3 8.7 8.7 4.8 6.0 8.4 6.7

15.0 10.9 9.9 8.9 5.6 5.6 8.1 5.9

7.1 7.2 8.1 8.1 14.0 12.2 8.6 11.1

−1.5 4.7 6.2 7.8 12.8 12.8 9.1 12.4

7.6 − − − − − − −

10.7 − − − − − − −

9.8 − − − − − − −

5.0 − − − − − − −

δH was calculated using the GIAOs method49 implemented in the Qsite50 program with the unrestricted DFT method with the B3LYP functional and LACVP** basis sets. − , not applicable. bOnly W539 is present in the O4-water chain. a

1927



Perspective

Figure 3. pKa(O−H/O−) of each OH group of the O4-water chain in S0 and S1. (a) The H-bond geometry before proton transfer occurs (the “pre-PT” H-bond pattern). OH groups that can and cannot change orientations in the proton transfer are indicated by red and blue lines and balls, respectively. (b) The pKa levels in S0 (black dotted lines) and S1 (red solid lines and labels) when the proton is localized at O4 (i.e., O4 = OH−, pre-PT). The blue thick arrows indicate the decrease in pKa in the donor O4 site due to the presence of the O4-water chain from the value in the absence of the O4-water chain (with only W539). The blue thin arrows indicate the downhill proton transfer in S1. (c) The H-bond geometry after proton transfer occurs (the “post-PT” H-bond pattern). 1928



Perspective

The H-bond network of the O5 path (Figure 1b) resembles case 1, which suggests that proton transfer occurs with the localized charge-transfer model, because OH− at O5 has no stable H-bond acceptor7,17−19 owing to the presence of conserved hydrophobic D1-Val185. However, the localized charge-transfer model is excluded from the proton-transfer mechanism of the O4-water chain, because all the water molecules form a continuous H-bond network in the recent high-resolution crystal structures.17,18 Intriguingly, in the S0−S1 transition, the H-bonded network [O4−H···OW539−H···OW538−H···OW393] resulted in a decrease in pKa(O4−H/O4−) by 8.6, pKa(OW539−H/OW539−) by 2.5, and pKa(OW538−H/OW538−) by 1.9 (Table 1, Figure 3a), suggesting that all three H atoms in [O4−H···OW539−H··· OW538−H···OW393] concertedly migrated toward the acceptor moieties in S1. This is the same number of water molecules involved in the delocalized soliton-transfer model (i.e., only 3−5 water molecules38). It seems likely that the mechanism of proton transfer along the O4-water chain in the S0−S1 transition resembles that of the delocalized soliton-transfer model.38 (Note: the pKa values listed in Table 1 and Figure 3a are for the case where the proton is still in the O4 moiety; as the proton moves, the pKa values in the O4-water chain will be updated accordingly.) These features are consistent with the known characteristics of the S0−S1 transition, rationalized as a rate-limiting electron transfer followed by a deprotonation step, with its rate insensitive to H2O/D2O exchange, and its activation energy being lower than that of the S2−S3 transition.22−24 Design and Roles of the Proton-Conducting Media. Figure 3a shows that the O−H groups that are not along the O4-water chain have always significantly higher pKa (5 to 10 pKa units) than the other O−H groups of H2O whose H-bond acceptor groups are mostly nontitratable polar groups. Thus, the proton predominantly transfers along the chain. If proton transfer occurs with the delocalized soliton-transfer mechanism,38 removal of strongly H-bonded water molecules from the O4-water chain should alter the energy profile of the proton transfer. Intriguingly, the removal of all of the water molecules except W539 (i.e., 7 water molecules: W538, W393, ..., and W399) leads to a significant pKa upshift at O4 by ∼6 in S1, even if the proton acceptor W539 still existed (Table 1, Figure 3b). The PSII crystal structures17,18 show that O4 forms two μ-oxo bridges, O4−Mn3 and O4−Mn4. Thus, one of the reasons for the significantly lowered pKa(O4−H/O4−) = −1.5 in S1 is that the Mn ion undergoing oxidation was Mn3 in the S0−S1 transition. However, the influence of the Mn3 oxidation on the pKa(O4−H/O4−) downshift in the S0−S1 transition is limited to 4.8 (= 9.8−5.0, “without O4-water chain” in Table 1), which cannot account for the entire pKa(O4−H/O4−) downshift of 8.6 [= 7.1 − (−1.5), “with O4-water chain” in Table 1] for the S0−S1 transition. The remaining pKa(O4−H/O4−) shift of 3.8 (= 8.6−4.8) should be explained as charge delocalization over (H2O)n, because unlike the redox-active Mn4CaO5 cluster, the net charge of the O4-water chain is zero. These results provide further support that the proton-transfer mechanism of the O4-water chain could be explained by the delocalized soliton-transfer model,38 where entire water molecules cooperatively enhance the O4−H bond elongation and proton release toward the water chain. As far as we are aware, the O4-water chain is the first example that clearly shows that a strongly H-bonded water chain not only serves as a mere proton-conducting wire but also significantly

As far as we are aware, the O4-water chain is the first example that clearly shows that a strongly H-bonded water chain not only serves as a mere proton-conducting wire but also significantly decreases pKa of the initial proton-releasing site, increasing the driving force for the downhill proton transfer. decreases pKa of the initial proton-releasing site, increasing the driving force for the downhill proton transfer. The absence of a strongly H-bonded water chain would be disadvantageous for proton transfer from the loss of these benefits, which is the case for the O5 path, where O5 has no H-bond partner. Further Proton Transfer Pathway via PsbU toward the Bulk Surface. In the 1.9 Å structure,17 the H-bond network of the water chain is terminated at W399 (Figure 3a). The region of W545, W1047, and W399 may serve as a proton reservoir for a proton released from Mn4CaO57, but further proton transfer toward the lumenal bulk surface may occur along a channel with the radius of ∼1.5 Å that connects with the protein bulk surface near PsbU-Tyr21 (PsbU channel, Figure 4). This channel resembles that previously proposed as a possible proton channel of PSII by Gabdulkhakov et al.39 Although the specific role of the protein subunit PsbU remains unclear, PsbU and PsbV are membrane-extrinsic protein subunits conserved in cyanobacteria but are replaced with PsbP and PsbQ in higher plants and green algae.40 Recent Fourier transform infrared studies suggest that PsbU and PsbV may regulate the conformation of the protein environment associated with the Mn4CaO5 cluster. The protein environment is correlated with the O2 evolution activity and the retention activity of Ca2+ and Cl− ions.41 In contrast to the region of the O4-water chain, the PsbU channel is not completely filled with water molecules (e.g., Figure 4). To analyze the possible distribution of water molecules in the vacant region of the PsbU channel, we used a three-dimensional reference interaction site model (3D-RISM) with Placevent analysis,42−45 as previously used for the inner channel of channelrhodopsin.46,47 The distribution pattern of water molecules obtained from the 3D-RISM with Placevent analysis is consistent with the positions of the eight water molecules identified in the 1.9 Å structure (Figure 5). Further 3D-RISM with Placevent analysis suggests that water molecules can also exist along the PsbU channel, even in the region where the water molecules are not seen in the crystal structure (Figure 5). The PSII crystal structures17,18 show a number of Asn residues (e.g., D1-Asn338, D2-Asn350, PsbO-Asn155, PsbUAsn99, and PsbU-Asn100; Figure 4) along the PsbU channel. Asn residues also exist as the conserved dual Asn-Pro-Ala motif in water channel of aquaporin (e.g., see ref 48). Therefore, it seems possible that water molecules exist that are not seen in the crystal structure irrespective of the resolution simply because they are too mobile. Then, the PsbU channel may represent a water reservoir, possibly for the O4-water chain functional in the water oxidation cycle. In the proton-conducting O4-water chain, one of the longest H-bonded straight water chains identified in protein crystal 1929



Perspective

Figure 4. (a) O4-water chain and the proceeding PsbU channel (blue mesh) that connect the Mn4CaO5 cluster with the protein bulk surface. The channel space was analyzed using the program CAVER starting from the O4 atom with the probe radius 0.4 Å.52 Water molecules identified in the 1.9 Å structure17 are depicted as red balls (left). PsbU-Tyr21, located near the protein surface of PsbU (right). (b) H-bond distances in the PsbU channel (in angstroms). 1930



Perspective

program (K.S.); JSPS KAKENHI (22740276 and 26800224 to K.S. and 15H00864, 26105012, and 26711008 to H.I.); Materials Integration for engineering polymers of Cross-ministerial Strategic Innovation Promotion Program (SIP, H.I.); Tokyo Ohka Foundation for the Promotion of Science and Technology (H.I.); and Interdisciplinary Computational Science Program in CCS, University of Tsukuba. Theoretical calculations were partly performed using Research Center for Computational Science, Okazaki, Japan.

■

(1) Renger, G. Photosynthetic water oxidation to molecular oxygen: apparatus and mechanism. Biochim. Biophys. Acta, Bioenerg. 2001, 1503, 210−28. (2) 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, 228−37. (3) 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, 140−53. (4) Vassiliev, S.; Zaraiskaya, T.; Bruce, D. Exploring the energetics of water permeation in photosystem II by multiple steered molecular dynamics simulations. Biochim. Biophys. Acta, Bioenerg. 2012, 1817, 1671−8. (5) 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, 15670−3. (6) Linke, K.; Ho, F. M. Water in Photosystem II: Structural, functional and mechanistic considerations. Biochim. Biophys. Acta, Bioenerg. 2014, 1837, 14−32. (7) Saito, K.; Rutherford, A. W.; Ishikita, H. Energetics of proton release on the first oxidation step in the water-oxidizing enzyme. Nat. Commun. 2015, 6, 8488. (8) Rapatskiy, L.; Cox, N.; Savitsky, A.; Ames, W. M.; Sander, J.; Nowaczyk, M. M.; Rögner, M.; Boussac, A.; Neese, F.; Messinger, J.; et al. Detection of the water-binding sites of the oxygen-evolving complex of Photosystem II using W-band 17O electron-electron double resonance-detected NMR spectroscopy. J. Am. Chem. Soc. 2012, 134, 16619−34. (9) McConnell, I. L.; Grigoryants, V. M.; Scholes, C. P.; Myers, W. K.; Chen, P. Y.; Whittaker, J. W.; Brudvig, G. W. EPR-ENDOR characterization of (17O, 1H, 2H) water in manganese catalase and its relevance to the oxygen-evolving complex of photosystem II. J. Am. Chem. Soc. 2012, 134, 1504−12. (10) Galstyan, A.; Robertazzi, A.; Knapp, E. W. Oxygen-evolving Mn cluster in photosystem II: the protonation pattern and oxidation state in the high-resolution crystal structure. J. Am. Chem. Soc. 2012, 134, 7442−9. (11) Cox, N.; Pantazis, D. A.; Neese, F.; Lubitz, W. Biological water oxidation. Acc. Chem. Res. 2013, 46, 1588−96. (12) Robblee, J. H.; Messinger, J.; Cinco, R. M.; McFarlane, K. L.; Fernandez, C.; Pizarro, S. A.; Sauer, K.; Yachandra, V. K. The Mn cluster in the S0 state of the oxygen-evolving complex of photosystem II studied by EXAFS spectroscopy: are there three di-μ-oxo-bridged Mn2 moieties in the tetranuclear Mn complex? J. Am. Chem. Soc. 2002, 124, 7459−7471. (13) Messinger, J. Evaluation of different mechanistic proposals for water oxidation in photosynthesis on the basis of Mn4OxCa structures for the catalytic site and spectroscopic data. Phys. Chem. Chem. Phys. 2004, 6, 4764−4771. (14) Kulik, L. V.; Epel, B.; Lubitz, W.; Messinger, J. Electronic structure of the Mn4OxCa cluster in the S0 and S2 states of the oxygenevolving complex of photosystem II based on pulse 55Mn-ENDOR and EPR spectroscopy. J. Am. Chem. Soc. 2007, 129, 13421−35. (15) Perez Navarro, M.; Ames, W. M.; Nilsson, H.; Lohmiller, T.; Pantazis, D. A.; Rapatskiy, L.; Nowaczyk, M. M.; Neese, F.; Boussac, A.; Messinger, J.; et al. Ammonia binding to the oxygen-evolving

Figure 5. Distribution pattern of water molecules (red mesh) in the O4-water chain and the PsbU channel, analyzed using 3D-RISM with Placevent analysis.42−45 The threshold of the distribution function was 4.5, which implies that the probability of finding water is 4.5 times greater than bulk. The positions of the water molecules in the 1.9 Å structure17 (red balls) are consistent with the obtained distribution pattern.

structures, proton transfer occurs in the S0−S1 transition and pKa downshifts along the continuous H-bond network (Figure 3, Table 1). The water chain provides a conducting media for protons and significantly decreases pKa of the proton donor moiety, facilitating the downhill proton transfer along the entire water chain. Loss of the corresponding water chain is disadvantageous for proton release from the proton-releasing site. This holds true for putative deprotonation at O5 of the Mn4CaO5 cluster (Figure 1), which has no stable H-bond partner because of the presence of a conserved hydrophobic amino acid side chain, D1-Val185, as identified in all of the recent high-resolution crystal structures of PSII.

■

ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jpclett.6b00656. Complete citation for ref 45, experimentally measured pKa values of 36 titratable molecules presented in Figure 2 (Table S1) (PDF)

■

REFERENCES

AUTHOR INFORMATION

Corresponding Author

*Tel.: +81-3-5452-5056. Fax: +81-3-5452-5083. E-mail: [email protected]. Notes

The authors declare no competing financial interest.

■

ACKNOWLEDGMENTS We thank Hirohi C. Watanabe and Ryo Hasegawa for useful discussions. This research was supported by the JST PRESTO 1931



Perspective

complex of photosystem II identifies the solvent-exchangeable oxygen bridge μ-oxo of the manganese tetramer. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 15561−6. (16) Zhang, C.; Chen, C.; Dong, H.; Shen, J. R.; Dau, H.; Zhao, J. Inorganic chemistry. A synthetic Mn4Ca-cluster mimicking the oxygenevolving center of photosynthesis. Science 2015, 348, 690−3. (17) 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. (18) Suga, M.; Akita, F.; Hirata, K.; Ueno, G.; Murakami, H.; Nakajima, Y.; Shimizu, T.; Yamashita, K.; Yamamoto, M.; Ago, H.; et al. Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses. Nature 2015, 517, 99−103. (19) Pal, R.; Negre, C. F.; Vogt, L.; Pokhrel, R.; Ertem, M. Z.; Brudvig, G. W.; Batista, V. S. S-State Model of the Oxygen-Evolving Complex of Photosystem II. Biochemistry 2013, 52, 7703−7706. (20) Siegbahn, P. E. Water oxidation mechanism in photosystem II, including oxidations, proton release pathways, O−O bond formation and O2 release. Biochim. Biophys. Acta, Bioenerg. 2013, 1827, 1003−19. (21) Dilbeck, P. L.; Bao, H.; Neveu, C. L.; Burnap, R. L. Perturbing the water cavity surrounding the manganese cluster by mutating the residue D1-valine 185 has a strong effect on the water oxidation mechanism of photosystem II. Biochemistry 2013, 52, 6824−33. (22) Renger, G.; Hanssum, B. Studies on the reaction coordinates of the water oxidase in PS II membrane fragments from spinach. FEBS Lett. 1992, 299, 28−32. (23) 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. (24) Haumann, M.; Bögershausen, O.; Cherepanov, D.; Ahlbrink, R.; Junge, W. Photosynthetic oxygen evolution: H/D isotope effects and the coupling between electron and proton transfer during the redox reactions at the oxidizing side of Photosystem II. Photosynth. Res. 1997, 51, 193−208. (25) Perrin, C. L.; Nielson, J. B. ″Strong″ hydrogen bonds in chemistry and biology. Annu. Rev. Phys. Chem. 1997, 48, 511−544. (26) Schutz, C. N.; Warshel, A. The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp··· His pair in serine proteases. Proteins: Struct., Funct., Genet. 2004, 55, 711−723. (27) Frey, P. A.; Whitt, S. A.; Tobin, J. B. A low-barrier hydrogen bond in the catalytic triad of serine proteases. Science 1994, 264, 1927−30. (28) Cleland, W. W.; Kreevoy, M. M. Low-barrier hydrogen bonds and enzymic catalysis. Science 1994, 264, 1887−1890. (29) Ishikita, H.; Saito, K. Proton transfer reactions and hydrogenbond networks in protein environments. J. R. Soc., Interface 2014, 11, 20130518. (30) Schmidt am Busch, M.; Knapp, E.-W. Accurate pK a determination for a heterogeneous group of organic molecules. ChemPhysChem 2004, 5, 1513−1522. (31) Galstyan, G.; Knapp, E. W. Computing pKA values of hexa-aqua transition metal complexes. J. Comput. Chem. 2015, 36, 69−78. (32) Robertazzi, A.; Galstyan, A.; Knapp, E. W. PSII manganese cluster: protonation of W2, O5, O4 and His337 in the S1 state explored by combined quantum chemical and electrostatic energy computations. Biochim. Biophys. Acta, Bioenerg. 2014, 1837, 1316−21. (33) Frey, P. A. In Isotope Effects in Chemistry and Biology; Kohen, A., Limbach, H.-H., Eds.; CRC Press, Boca Raton, FL, 2006; pp 975−993. (34) Saito, K.; Ishikita, H. Formation of an unusually short hydrogen bond in photoactive yellow protein. Biochim. Biophys. Acta, Bioenerg. 2013, 1827, 387−394. (35) Saito, K.; Ishikita, H. H atom positions and nuclear magnetic resonance chemical shifts of short H bonds in photoactive yellow protein. Biochemistry 2012, 51, 1171−7. (36) Limbach, H.-H.; Tolstoy, P. M.; Pérez-Hernández, N.; Guo, J.; Shenderovich, I. G.; Denisov, G. S. OHO hydrogen bond geometries and NMR chemical shifts: from equilibrium structures to geometric H/D isotope effects, with applications for water, protonated water, and compressed ice. Isr. J. Chem. 2009, 49, 199−216.

(37) Wikstrom, M.; Verkhovsky, M. I.; Hummer, G. Water-gated mechanism of proton translocation by cytochrome c oxidase. Biochim. Biophys. Acta, Bioenerg. 2003, 1604, 61−5. (38) Stuchebrukhov, A. A. Mechanisms of proton transfer in proteins: localized charge transfer versus delocalized soliton transfer. Phys. Rev. E Stat Nonlin Soft Matter Phys. 2009, 79, 031927. (39) Gabdulkhakov, A.; Guskov, A.; Broser, M.; Kern, J.; Muh, F.; Saenger, W.; Zouni, A. Probing the accessibility of the Mn4Ca cluster in photosystem II: channels calculation, noble gas derivatization, and cocrystallization with DMSO. Structure 2009, 17, 1223−34. (40) Ifuku, K.; Noguchi, T. Structural coupling of extrinsic proteins with the oxygen-evolving center in photosystem II. Front. Plant Sci. 2016, 7, 84. (41) Nagao, R.; Tomo, T.; Noguchi, T. Effects of extrinsic proteins on the protein conformation of the oxygen-evolving center in cyanobacterial photosystem II as revealed by Fourier transform infrared spectroscopy. Biochemistry 2015, 54, 2022−31. (42) Beglov, D.; Roux, B. An integral equation to describe the solvation of polar molecules in liquid water. J. Phys. Chem. B 1997, 101, 7821−7826. (43) Kovalenko, A.; Hirata, F. Potential of mean force between two molecular ions in a polar molecular solvent: a study by the threedimensional reference interaction site model. J. Phys. Chem. B 1999, 103, 7942−7957. (44) Luchko, T.; Gusarov, S.; Roe, D. R.; Simmerling, C.; Case, D. A.; Tuszynski, J.; Kovalenko, A. Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber. J. Chem. Theory Comput. 2010, 6, 607−624. (45) Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M., et al. AMBER 12; University of California: San Francisco, 2012. (46) Watanabe, H. C.; Welke, K.; Sindhikara, D. J.; Hegemann, P.; Elstner, M. Towards an understanding of channelrhodopsin function: simulations lead to novel insights of the channel mechanism. J. Mol. Biol. 2013, 425, 1795−814. (47) Wietek, J.; Wiegert, J. S.; Adeishvili, N.; Schneider, F.; Watanabe, H.; Tsunoda, S. P.; Vogt, A.; Elstner, M.; Oertner, T. G.; Hegemann, P. Conversion of channelrhodopsin into a light-gated chloride channel. Science 2014, 344, 409−12. (48) Wraight, C. A. Chance and design–proton transfer in water, channels and bioenergetic proteins. Biochim. Biophys. Acta, Bioenerg. 2006, 1757, 886−912. (49) Cao, Y.; Beachy, M. D.; Braden, D. A.; Morrill, L.; Ringnalda, M. N.; Friesner, R. A. Nuclear-magnetic-resonance shielding constants calculated by pseudospectral methods. J. Chem. Phys. 2005, 122, 224116. (50) QSite, version 5.8; Schrödinger, LLC: New York, 2012. (51) Jaguar, version 7.9, Schrödinger, LLC: New York, 2012. (52) Petrek, M.; Otyepka, M.; Banas, P.; Kosinova, P.; Koca, J.; Damborsky, J. CAVER: A new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinf. 2006, 7, 316.

1932


of a Proton-Conducting Water Chain in ... - ACS Publications

Recommend Documents