Article pubs.acs.org/biochemistry
Structural Factors That Alter the Redox Potential of Quinones in Cyanobacterial and Plant Photosystem I Keisuke Kawashima† 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
‡
S Supporting Information *
ABSTRACT: Using the cyanobacterial and plant photosystem I (PSI) crystal structures and by considering the protonation states of all titratable residues, redox potentials (Em) of the two phylloquinones A1A and A1Bwere calculated. The calculated Em values were Em(A1A) = −773 mV and Em(A1B) = −818 mV for the plant PSI structure and Em(A1A) = −612 mV and Em(A1B) = −719 mV for the cyanobacterial PSI structure. Our analysis of the PSI crystal structures suggested that the side-chain orientations of Lys-B542 and Gln-B678 in the cyanobacterial crystal structure differ from these side-chain orientations in the plant crystal structure. Quantum mechanical/molecular mechanical calculations indicated that the geometry of the cyanobacterial PSI crystal structure was best described as the conformation where Asp-B575 is protonated and A1A is reduced to A1A•−, which might represent the high-potential A1A form (Rutherford, A. W., Osyczka, A., Rappaport, F. (2012) FEBS Lett. 586, 603−616). Reorienting the Lys-B542 and Gln-B678 sidechains and rearranging the H-bond pattern of the water cluster near Asp-B575 lowered the Em to Em(A1A) = −718 mV and Em(A1B) = −795 mV. It seems possible that PSI has two conformations: the high-potential A1A form and the low-potential A1A form.
T
he photosynthetic reaction center of photosystem I (PSI) is composed of the PsaA/PsaB heterodimeric protein subunit pair and the PsaC subunit, which harbor the chlorophyll pair PA/PB, where PB is chlorophyll a (Chla) and PA is Chla’, (i.e., the 132 epimer of Chla);1 the accessory Chla pair A−1A/A−1B; the electron acceptor Chla pair A0A/A0B, which corresponds to the pheophytin pair in photosystem II; the phylloquinone pair A1A/A1B; and the iron sulfur clusters FX, FA, and FB (Figure 1). These cofactors form two electron transfer chains along the pseudo-C2 axis.2−5 Ultrafast transient absorption studies suggested that the accessory Chla (ec22 or A−1) in PSI may be the primary electron donor in charge separation on the two branches of electron transfer.6−11 Further electron transfer occurs from A1•− to FX. Reoxidation of A1•− by the electron acceptor FX occurs biphasically with the time constants of ∼20 and ∼150 ns.3 The redox potential (Em) values of A1 are estimated from kinetic measurements to be −810 mV12 and −754 mV13 for spinach PSI; lower than −700 mV;3 and Em(A1A) = −635 mV and Em(A1B) = −690 mV for PSI from Synechocystis sp. PCC 6803 (assuming Em(FX) = −680 mV and the reorganization energy λ = 0.7 eV for forward electron transfer from A1 to FX).14 Alternatively, the calculated Em(A1A) and Em(A1B) were −531 and −686 mV, respectively, for PSI from Thermosynechococcus elongatus when water molecules were represented implicitly with the dielectric constant εw = 80, using Em = −465 mV in DMF versus NHE15 as the reference Em value for © XXXX American Chemical Society
Figure 1. Electron transfer chains identified in the cyanobacterial PSI crystal structure.2 Clusters of water molecules near A1A and A1B are depicted in yellow and magenta, respectively.
phylloquinone.16 The Em(A1A) and Em(A1B) were −639 and −776 mV, respectively, when water molecules identified in the crystal structure were considered explicitly.16 More negative values were calculated to be Em(A1A) = −671 mV and Em(A1B) Received: February 1, 2017 Revised: May 18, 2017 Published: May 22, 2017 A
DOI: 10.1021/acs.biochem.7b00082 Biochemistry XXXX, XXX, XXX−XXX
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Biochemistry = −844 mV, when it was assumed that Em = −800 mV in DMF versus NHE as the reference Em value for phylloquinone.17 These reported Em(A1) values are low with respect to an Em of −150 mV for the same quinone species at the QA binding site in bacterial photosynthetic reaction centers from Blastochloris viridis. 3 The difference in the net charge between F X ([Fe4S4(Cys)4)]2−) and the non-heme Fe cluster ([Fe(His)4(Glu)]+) is responsible for the difference of ∼500 mV between PSI and bacterial photosynthetic reaction centers.16 The following two factors are responsible for Em(A1A) being greater than Em(A1B): (i) protonation of Asp-B575; protonation of Asp-B575 occurred in response to formation of A1A•−, leading to an increase in Em(A1A) with respect to Em(A1B),16,18 and (ii) different orientations of the backbone carbonyl O atoms in the Ser-A692/Ser-B672 pair; this shortens the distance between A1B and the Ser-B672 backbone carbonyl group (OA1B...OSer‑B672 = 4.0 Å) with respect to the distance between A1A and the Ser-A692 backbone carbonyl group (OA1A...OSer‑A692 = 6.3 Å),2 thereby decreasing Em(A1B) with respect to Em(A1A).16 Asp-B575 forms an H-bond with a cluster of water molecules identified near A1B in the cyanobacterial PSI crystal structure.2 Since Asp-B575 is the only ionizable residue that is situated between A1A and A1B (Figure 1), protonation of Asp-B575 could affect Em(A1A) significantly, as was suggested in theoretical studies.16,18 However, the cyanobacterial PSI crystal structure shows that Asp-B575 is neither exposed to the protein bulk surface nor linked with proton transfer pathways that connect with the protein bulk surface.2 The absence of proton transfer pathways suggests that proton transfer to Asp-B575 may not be fast enough to occur within the lifetime of A1•−. A cluster of water molecules may help stabilize the ionized or protonated state of Asp-B575 (i.e., deprotonation or protonation events of Asp-B575) by rearranging the H-bond patterns. The presence of the water cluster near A1B was first reported in the cyanobacterial PSI crystal structure from T. elongatus at a resolution of 2.5 Å.2 The corresponding water cluster was also identified in the plant PSI crystal structure from Pisum sativum at a resolution of 2.8 Å.19,20 Thus far, the cyanobacterial 2.5 Å structure2 has the highest resolution, but, to our knowledge, the electron density map has not been reported. On the other hand, an electron density map has been reported for the plant 2.8 Å structure.19 This allows us to analyze possible structural differences between the two crystal structures. However, at a level of 2.5−2.8 Å resolutions, a clear discrimination, e.g., between the −NH2 and −CO groups of Gln side-chain, based on the electron density map is not possible. The difference in side-chain orientations and conformations may result in a difference in Em(A1). Here, we report calculated Em(A1A) and Em(A1B) values, using the cyanobacterial2 and plant19 PSI crystal structures, solving the linear Poisson−Boltzmann equation, and considering the protonation states of all titratable sites in the entire PSI proteins. The energetically stable side-chain orientations and conformations were also evaluated using a quantum mechanical/molecular mechanical (QM/MM) approach.
with CHARMM,21 whereas the positions of all non-hydrogen atoms were fixed, and all titratable groups were kept in their standard protonation states (i.e., acidic groups were ionized and basic groups were protonated). All Chla molecules and phylloquinones were kept in the neutral charge state, and Fe4S4 clusters were kept in the oxidized state. For QM/MM calculations, we added additional counterions to neutralize the system. Atomic Partial Charges. Atomic partial charges of the amino acids were adopted from the all-atom CHARMM2222 parameter set. The atomic charges of Chla, phylloquinone, βcarotene, 1,2-distearoyl-monogalactosyl-diglyceride (LMG), and digalactosyl-diacyl-glycerol (DGDG) were determined by fitting the electrostatic potential in the neighborhood of these molecules using the RESP procedure.23 The electronic wave functions were calculated after geometry optimization by the restricted density functional theory (DFT) method (except for reduced phylloquinone and charged Chla, which were optimized by the unrestricted DFT method), with the B3LYP functional and 6-31G** basis sets, using the JAGUAR program.24 The atomic charges of the Fe4S4 clusters were obtained from previous studies.25 The atomic charges of the headgroup of 1,2-dipalmitoyl-phosphatidyl-glycerole (LHG) were obtained from the CHARMM2222 parameter set. LHG was treated as being ionized with the net charge of −1 (e.g., the titratable O atom of LHG near A1A forms an H-bond with the Ser-A723 side-chain (OLHG−OSer‑A723 = 2.7 Å) in the cyanobacterial PSI structure).2 Notably, the presence of positively charged Arg-A575 (OLHG−NArg‑A575 = 4.2 Å) seems to stabilize the ionized form of LHG near A1A (Tables S1−S6). Em Calculation: Solving the Linear Poisson−Boltzmann Equation. The present computation was based on the electrostatic continuum model, wherein we solved the linear Poisson−Boltzmann equation with the MEAD program.26 PB was kept in the cationic Chla•+ state to approximate the [PA/ PB]•+ state,27−29 and the other Chla were kept in the neutral charge states. Phylloquinone and Fe4S4 clusters were in the oxidized states during the redox titration of each phylloquinone. Em = −465 mV was reported for one-electron reduction of menaquinone-10 in DMF versus NHE15 (see also ref 3). In the present study, we used the value of −405 mV as a reference Em value for phylloquinone. To obtain the absolute Em values of phylloquinone in the protein environment, we calculated the electrostatic energy difference between the two redox states in a reference model system. The difference in the Em value of the protein relative to the reference system was added to the known Em value. All other titratable sites were fully equilibrated to the phylloquinone redox state during titration. The ensemble of the protonation patterns was sampled by the Monte Carlo method with the Karlsberg30 program code. The dielectric constants were set to εp = 4 inside the protein and εw = 80 for water. All computations were performed at 300 K, pH 7.0, and an ionic strength of 100 mM. The linear Poisson−Boltzmann equation was solved using a three-step grid-focusing procedure at resolutions of 2.5 Å, 1.0 Å, and 0.25 Å. Monte Carlo sampling yielded the probabilities [Aox] and [Ared] of the two redox states of molecule A. Em was evaluated using the Nernst equation. A bias potential was applied to obtain an equal amount of both redox states ([Aox] = [Ared]), thereby yielding Em as the resulting bias potential. Possible Problems Using Molecular Dynamics Simulations in Em Calculations. Molecular dynamics (MD) simulations can sample the conformational ensembles. MD
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EXPERIMENTAL DETAILS Coordinates. The atomic coordinates of PSI were taken from the X-ray structures of cyanobacterial PSI from T. elongatus at 2.5 Å resolution (PDB code, 1JB0)2 and plant PSI from P. sativum at 2.8 Å resolution (PDB code, 4XK8).19 Hydrogen atoms were generated and energetically optimized B
DOI: 10.1021/acs.biochem.7b00082 Biochemistry XXXX, XXX, XXX−XXX
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Biochemistry simulations are typically performed in the fixed protonation states of the titratable residues and the fixed redox states of the redox active groups. As recently demonstrated,31 fixation of the protonation states of titratable residues can be problematic when using an MD-based approach to calculate the Em value, because the protein structure changes with respect to the original atomic coordinates of the crystal structure, to reproduce the initially considered single protonation pattern of the titratable residues. In addition, the protonation states of some titratable residues (e.g., Asp-B575 in the present study) can be strongly coupled with the redox state of the redox active cofactor (e.g., A1A), and affects the Em value, which can often explain the pH-dependence of the Em for redox active groups.32−34 Fixation of the protonation states of the titratable groups, e.g., to be ionized should also overstabilize the oxidized state of the redox active groups and lower the Em value. Thus, for Em calculations of redox-active proteins, which have titratable groups, it is a prerequisite to reproduce the Henderson−Hasselbalch curve for the titratable residues.35 This can be achieved only when the partial protonation states of the titratable groups are appropriately considered, as demonstrated in a number of electrostatic approaches (e.g., refs 32−34). QM/MM Calculations. We employed the electrostatic embedding QM/MM scheme, in which electrostatic and steric effects created by a protein environment were explicitly considered, and we used the Qsite36 program code. We employed the restricted DFT method with the B3LYP functional and LACVP** basis sets. To refine the cyanobacterial Lys-B542 moiety, the QM region was defined as the sidechains of Lys-B418, Lys-B542, Asp-B546, Ser-B550, Lys-B556, and Glu-A699 and the backbone of Tyr-A696, whereas other protein units and all cofactors were approximated by the MM force field. To refine the cyanobacterial Gln-B678 moiety, the QM region was defined as the side-chains of Gln-B678, GluB682, and Tyr-C80 and the backbones of Pro-B703, Val-B704, and Ala-B705. To analyze the cyanobacterial Asp-B575 moiety, the QM region was defined as the side-chains of Asp-B575, Tyr-B583, and Arg-B712 and the water molecules B5018, B5019, B5030, B5055, B5056, and B5058. The geometries were refined by constrained QM/MM optimization. Specifically, the coordinates of the heavy atoms in the surrounding MM region were fixed at their original X-ray coordinates, while those of the H atoms in the MM region were optimized using the OPLS2005 force field. All the atomic coordinates in the QM region were fully relaxed (i.e., not fixed) in the QM/MM calculation. See Supporting Information for the atomic coordinates of the resulting QM region. Analysis of Water Molecule Distribution in the Protein. To analyze the distribution of water molecules in the PSI protein environment, we used a three-dimensional reference interaction site model (3D-RISM) with Placevent analysis,37−41 as previously used for the inner channel of channelrhodopsin42,43 and PSII.44 It should be noted that the distribution pattern of water molecules obtained from the 3DRISM with Placevent analysis was consistent with the positions of the water molecules.44
lower than Em(A1A) = −612 mV and Em(A1B) = −719 mV for the cyanobacterial PSI crystal structure (Table 1). Table 1. Em(A1A) and Em(A1B) Calculated Using the Original Geometries of the Plant19 and Cyanobacterial 2 PSI Crystal Structures (in mV) plant Em crystal structure uncharged PSI volume quinone in water Em shift (water to protein) due to protein charge due to loss of solvation
cyanobacteria
A1A
A1B
A1A
A1B
−773 −781 −405 −368 8 −376
−818 −797 −405 −413 −21 −392
−612 −789 −405 −207 177 −384
−719 −794 −405 −314 75 −389
When Em(A1A) and Em(A1B) were calculated in the uncharged PSI protein volume (i.e., in the absence of all atomic partial charges of the PSI protein), Em(A1A) and Em(A1B) ranged between −781 mV and −797 mV in both cyanobacterial and plant PSI structures, and they essentially possess the same value (Table 1). This indicates that the contributions of PSI protein volume to Em(A1A) and Em(A1B), which prevents solvation of reduced phylloquinone and thus lowers Em, were the same in both cyanobacterial and plant PSI structures. The difference in contributions of the protein atomic charges are predominantly responsible for the Em difference between the two PSI crystal structures (Table 1). Factors that Lower Em(A1) in Plant PSI with Respect to Cyanobacterial PSI. We calculated contributions of residues to Em(A1A) and Em(A1B) and identified the residues that increase Em(A1A) and Em(A1B) in cyanobacterial PSI with respect to plant PSI (Tables 2 and 3). Remarkably, these Table 2. Conserved Residues That Increase Em(A1A) in Cyanobacterial PSI with Respect to Plant PSI (in mV) cyanobacteria
Em(A1A) shift
plant
Em(A1A) shift
difference in Em(A1A) shift
Arg-A694 Lys-B542 Arg-A720 Lys-B418
254 178 81 53
Arg-A697 Lys-B536 Arg-A723 Lys-B415
196 124 38 22
59 54 43 30
Table 3. Conserved Residues That Increase Em(A1B) in the Cyanobacterial PSI Crystal Structure with Respect to the Plant PSI Crystal Structure (in mV) cyanobacteria
Em(A1B) shift
plant
Em(A1B) shift
difference in Em(A1B) shift
Gln-B678 Glu-B682 Asn-A445
33 −78 5
Gln-B672 Glu-B676 Asn-A447
−20 −110 −14
53 31 20
residues were mostly conserved in the two species, having the same net charge. This would suggest that either the conformation (e.g., side-chain orientations) or the shape of the protein bulk surface may differ between the two PSI structures. The following are the factors that we identified as altering Em between the cyanobacterial and plant PSI crystal structures. Cyanobacterial Lys-B542 Increases Em(A1A) with Respect to Plant Lys-B536: Difference in the Distance from A1A. LysB542 increases Em(A1A) in cyanobacterial PSI by 54 mV with
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RESULTS Em(A1A) and Em(A1B) Obtained Using the Original Cyanobacterial and Plant Structures. The calculated Em values were Em(A1A) = −773 mV and Em(A1B) = −818 mV for the plant PSI crystal structure, which were ∼100−160 mV C
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Biochemistry respect to Lys-B536 in plant PSI, irrespective of both being conserved, positively charged residues (Table 2). In the plant PSI structure, the Lys-B536 side-chain is oriented away from A1A (OLys‑B542−OA1A = 13.0 Å), whereas in the cyanobacterial PSI structure, the Lys-B542 side-chain is oriented toward A1A (OLys‑B542−OA1A = 10.7 Å). In the cyanobacterial PSI crystal structure, the positively charged Lys-B542 can stabilize A1A•− more effectively and increase Em(A1A) in cyanobacterial PSI with respect to plant PSI. Particularly for PSI, the electrostatic influence seems to be pronounced at the A1A and A1B binding sites in the protein inner core formed by the transmembrane helices (Figure 2).
Table 4. Evaluation of the Side-Chain Orientations in the Cyanobacterial PSI Crystal Structure (PDB Code, 1JB0)a RMSD Lys-B542 in the cyanobacterial PSI structure original orientation plant orientation Gln-B678 in the cyanobacterial PSI structure original orientation plant orientation
0.31b 0.28b 0.36c 0.14c
a
RMSD = root-mean-square deviation; original orientation = the sidechain orientation in the cyanobacterial PSI crystal structure; plant orientation = the side-chain orientation in the plant PSI crystal structure (PDB code, 4XK8). bThe QM region (i.e., quantumchemically treated region) was defined as residues in the H-bond network of Lys-B542 (i.e., side-chains of Glu-A699, Lys-B418, LysB542, Asp-B546, Ser-B550, and Lys-B556, and a backbone of TyrA696). The Lys-B542 side-chain, which was QM/MM-optimized, was excluded from RMSD calculations. cThe QM region was defined as residues in the H-bond network of Gln-B678 (i.e., side-chains of GlnB678, Glu-B682, and Tyr-C80, backbones of Val-B704 and Ala-B705, and the entire Pro-B703). The Gln-B678 side-chain, which was QM/ MM-optimized, was excluded from RMSD calculations.
Cyanobacterial Gln-B678 Orientation Increases Em(A1B) with Respect to Plant Gln-B672: Difference in H-Bond Network Energetics. Gln-B678 increases Em(A1B) in cyanobacterial PSI by 53 mV with respect to Gln-B672 in plant PSI (Table 3). We found that the Gln side-chain orientations are completely opposite in the two PSI crystal structures (Figure 3). The side-chain orientation of Gln-B678 in the original
Figure 2. Differences in side-chain orientations between plant LysB536 and cyanobacterial Lys-B542. (a) Lys-B536 in plant PSI. Dotted arrows indicate salt-bridges with Lys-B536. (b) The electron density map in the neighborhood of plant Lys-B536 (blue mesh). (c) LysB542 in cyanobacterial PSI. To the best of our knowledge, the electron density map has not been reported for the cyanobacterial PSI crystal structure (PDB code 1JB0).
In the plant PSI structure, Lys-B536 is oriented toward GluA702 and Asp-B540, forming two salt-bridges (NLys‑B536− OGlu‑A702 = 2.6 Å and NLys‑B536−OAsp‑B540 = 2.9 Å, Figure 2a). The electron density map also confirms the orientation of the plant Lys-B536 side-chain, which is stabilized by the two saltbridges (Figure 2b). In contrast, the corresponding salt-bridges are absent in the cyanobacterial PSI crystal structure (Figure 2c). In the cyanobacterial PSI crystal structure, Lys-B542 forms an H-bond with the backbone carbonyl group of Tyr-A696 (NLys‑B542−OTyr‑A696;‑CO = 2.5 Å), but the side-chain geometry seemingly does not allow Lys-B542 to form H-bonds with GluA699 and Asp-B546. It seems likely that the plant Lys-B536 conformation is more energetically stabilized than the cyanobacterial Lys-B542 conformation in terms of the number of salt-bridges. To the best of our knowledge, the electron density map has not been reported for the cyanobacterial PSI crystal structure (PDB code, 1JB0). Thus, to evaluate the Lys-B542 conformation, we calculated the root-mean-square deviation (RMSD) of the QM/MM-optimized structure with respect to the original cyanobacterial PSI crystal structure. The resulting RMSD of cyanobacterial Lys-B542 in the cyanobacterial PSI crystal structure was 0.31 Å for the original Lys-B542 conformation and 0.28 Å for the plant Lys-B536 conformation (Table 4). The similar RMSD suggests that Lys-B542 may also be able to adopt the plant Lys-B536 orientation in the geometry of the cyanobacterial PSI structure.
Figure 3. Differences in side-chain orientations between plant GlnB672 and cyanobacterial Gln-B678. (a) Gln-B672 in the plant PSI structure. (b) Gln-B678 in the cyanobacterial PSI structure. Dotted arrows indicate interactions between polar atoms.
cyanobacterial PSI crystal structure seems to be energetically unfavorable owing to repulsion with the backbone amide group of Ala-B705. It should be noted that at a level of 2.5−2.8 Å resolution, a clear discrimination between the O and N sites of the Gln side-chain in the electron density map is not possible. We calculated the RMSD of the QM/MM-optimized structure with respect to the original cyanobacterial crystal structure, considering both the cyanobacterial and plant orientations of the Gln side-chain. The resulting RMSD was significantly lower in the plant Gln-B672 orientation than the cyanobacterial Gln-B678 orientation, even in the cyanobacterial PSI crystal structure (Table 4). This suggests that the sidechain orientation of plant Gln-B672 is more energetically D
DOI: 10.1021/acs.biochem.7b00082 Biochemistry XXXX, XXX, XXX−XXX
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Biochemistry favorable, and Em(A1A) and Em(A1B) of cyanobacterial PSI should also be calculated using the side-chain orientation of plant Gln-B672. Cyanobacterial Arg-A694 Increases Em(A1A) with Respect to Plant Arg-A697: Difference in the Protein Bulk Surface of PsaE. Arg-A694 increases Em(A1A) in cyanobacterial PSI by 59 mV with respect to Arg-A697 in plant PSI (Table 2). However, neither the orientations of the two Arg side-chains nor the distances from A1A differ in the plant (NArg‑A697−OA1A = 6.5 Å) and cyanobacterial (NArg‑A694−OA1A = 6.3 Å) PSI crystal structures. We analyzed the distribution pattern of water molecules near the Arg residue, using the cyanobacterial and plant PSI crystal structures. Remarkably, the possible distribution of water molecules was identified near plant ArgA697 in calculations using the plant PSI crystal structure (Figure 4). However, the corresponding water distribution
the influence of cyanobacterial Arg-A720 (Table 2 and Figure 4). Protonation of Asp-B575 in the Cyanobacterial Crystal Structure. Protonation states of the PSI titratable sites as calculated by solving the Poisson−Boltzmann equation showed that cyanobacterial Asp-B575 and plant Asp-B569 were essentially ionized when A1A and A1B were oxidized. However, Asp-B575 and Asp-B569 were protonated in response to formation of A1A•−, even in the presence of clusters of explicit water molecules near A1A and A1B (Table 5), as already Table 5. Protonation States of Cyanobacterial Asp-B575 and Plant Asp-B569 Calculated Solving the Poisson−Boltzmann Equation (in [H+]) redox states A1A0A1B0
A1A−0.5A1B0
A1A0A1B−0.5
0.00 0.00
0.48 0.08
0.08 0.00
0.00
0.36
0.03
cyanobacterial PSI refined structure plant PSI
reported.16,18 Notably, the calculated water distribution pattern near A1A and A1B was identical to the positions of clusters of water molecules in the cyanobacterial PSI crystal structure (Figure 5a). In addition, the low B-factor values of the water
Figure 4. Distribution pattern of water molecules near the plant PsaE protein subunit (green) calculated for the plant PSI structure (blue mesh). For comparison, the cyanobacterial PsaE protein subunit (orange) is superimposed. The CD-loop of PsaE in the cyanobacterial PSI structure is longer than this loop in the plant PSI crystal structure, which results in the absence of water molecules distributed in the corresponding region of the cyanobacterial PSI structure. The threshold of 3D distribution functions is 1.0.
cannot be identified in cyanobacterial Arg-A694 in the cyanobacterial PSI crystal structure. This is because of the difference in the length of the CD-loop region of the PsaE protein subunit between the plant and cyanobacterial PSI structures. The CD-loop region (PsaE-40 to -56) in the cyanobacterial PsaE protein subunit is longer than this loop region in the plant PsaE protein,45,46 because of the inserted region, PsaE 47−54. The absence of the inserted region in plant PsaE results in the distribution of water molecules in the corresponding region (Figure 4), shielding electrostatic interactions of plant Arg-A697 with A1A in the plant PSI crystal structure with respect to the cyanobacterial PSI crystal structure. Thus, the influence of plant Arg-A697 on Em(A1A) is weaker than the influence of cyanobacterial Arg-A694, irrespective of their same net charge and nearly identical locations with respect to A1A (Table 2). This can also explain why the influence of plant Arg-A723 on Em(A1A) is weaker than
Figure 5. Distribution of water molecules near A1A and A1B (blue mesh), calculated using the cyanobacterial PSI structure. The O atoms of water molecule clusters near A1A and A1B identified in the original cyanobacterial PSI structure are depicted as red balls. (a) Side view. (b) Distant view.
clusters (mostly 20−30) suggest that water molecules near A1A and A1B should be considered as explicit water molecules with the fixed H-bond pattern, as treated in the present study. It seems more likely that the observed protonation of AspB575 (Table 5) originates from the geometry of the original cyanobacterial PSI crystal structure. In the cyanobacterial crystal structure, Asp-B575 has an H-bond partner, H2OB5018, in the water cluster near A1A (Figure 5a). QM/MM calculations E
DOI: 10.1021/acs.biochem.7b00082 Biochemistry XXXX, XXX, XXX−XXX
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Biochemistry
Figure 6. Geometry of the cluster of water molecules near Asp-B575 in cyanobacterial PSI. (a) The original cyanobacterial crystal structure.2 Bfactors are 20.3 for B5018, 17.9 for B5019, 20.7 for B5030, 36.2 for B5055, 29.9 for B5056, and 32.9 for B5058.2 (b) QM/MM-optimized geometry with ionized Asp-B575 and neutral A1A. (c) QM/MM-optimized geometry with ionized Asp-B575 and reduced A1A•−. (d) QM/MM-optimized geometry with Asp-B575 protonated at Oδ2 and reduced A1A•−. Dotted lines indicate H-bonds with Asp-B575.
Figure 7. Difference in the distance between the A1 carbonyl O site and the serine backbone carbonyl group in the j-jk loop that connects transmembrane helix (TMH) j with α-helix jk. (a) A1B binding site. (b) A1A binding site. The PsaA protein and A1A are depicted in yellow, whereas the PsaB protein and A1B are depicted in cyan. Red dotted lines indicate the distance between the A1 carbonyl O site and the serine backbone carbonyl group. (c) A water molecule, A5043, an H-bond partner of the backbone carbonyl group of Ser-A692. The blue dotted line indicates an Hbond.
resulted in OAsp‑B575−OB5018 distances of < ∼2.7 Å when AspB575 was considered to be ionized (Figure 6b,c). However, the cyanobacterial PSI crystal structure shows two asymmetric and long H-bond distances, 2.81 and 3.33 Å, inconsistent with the QM/MM geometry obtained in the presence of ionized AspB575. On the other hand, QM/MM calculations resulted in the OAsp‑B575−OB5018 distances of 2.65 and 3.30 Å when Asp-B575 was considered to be protonated in the A1A•− state (Figure 6d), which are closer to 2.81 and 3.33 Å in the original cyanobacterial PSI crystal structure (Figure 6a) and 2.65 and 3.09 Å in the plant PSI crystal structure.19 Notably, the resulting RMSD was the lowest among all possible protonation and redox states (Figure 6). These results suggest that the cyanobacterial PSI crystal structure2 is best interpreted as being the conformation with protonated Asp-B575 and reduced A1A. Cyanobacterial Trp-B673 and the Different Orientation of the Ser-A692/Ser-B672 Backbone Carbonyl Group. In the cyanobacterial PSI structure, the distance between the A1A carbonyl O site and the backbone carbonyl O atom of Ser-A692 is 6.3 Å, whereas the distance between the A1B carbonyl O site and the backbone carbonyl O atom of Ser-
B672 is shorter, 4.0 Å (Figure 7a,b). The present study suggests that the proximity of the carbonyl O atom of Ser-B672 to A1B destabilizes A1B•− and lowers Em(A1B) with respect to Em(A1A) by 55 mV. The shorter OSer‑B672;‑CO−OA1B distance in the SerA692/Ser-B672 pair originates from the different orientations in the backbone carbonyl groups of Ser-A692 and Ser-B672. The residue next to Ser-A692 is Gly-A693, whereas the residue next to Ser-B672 is Trp-B673. The bulky Trp-B673 side-chain seems to have been excluded from the A1B site to avoid steric repulsion with phylloquinone, resulting in a twisted backbone of the carbonyl group in the next Ser-B672 residue.2 This backbone twist seems to be energetically allowed because [SerA692···Gly-A693] and [Ser-B672···Trp-B673] are located in the loop region (j-jk loop) that connects transmembrane helix j with α-helix jk (Figure 7). The untwisted backbone carbonyl of Ser-A692 forms an H-bond with a cluster of water molecules near A1A, whereas the H-bond partner of the twisted Ser-B672 was not identified in the cyanobacterial PSI structure (Figure 7c); this may again suggest that the twist at Ser-B672 occurred mainly to avoid steric repulsion. F
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Biochemistry Table 7. Em(A1A) and Em(A1B) Calculated Using the Modified PSI Structures (in mV)a
The corresponding twist of the backbone carbonyl group (plant Ser-B666) was also identified in the plant PSI structure.19 Theoretical calculations suggested that Trp-B673 has no direct electrostatic influence on Em(A1B).16 On the other hand, it was proposed that minor structural differences between Gly-A693 and Trp-B673 might cause a significant Em difference between A1A and A1B.47 Mutating Trp-B673 to Gly in PSI from Chlamydomonas reinhardtii (i.e., Trp-B669) significantly decreases the rate of the forward electron transfer from A1B•− to FX, which was interpreted as an increase in Em(A1B) following this mutation.48 The present analysis suggests that the absence of the backbone carbonyl twist of Ser-B672 toward A1B is the reason for the specifically increased Em(A1B) in the W(B673)G mutant.
cyanobacteria
cyanobacteria A1B −795 −794 −405 −390 −1 −389
−612 −620 −607 −685 −716 −688 −718
−719 −715 −776 −730 −733 −792 −795
B678 (Figure 3) side-chains and rearranging the H-bond pattern of the cluster of molecules near Asp-B575 (Figure 6). The resolution of the plant PSI crystal structure (2.8 Å19) is lower than the resolution of the cyanobacterial PSI structure (2.5 Å2), while the assignment of the atoms in the plant PSI structure seems to be reasonable in terms of the reported electron density map. Considering the structural uncertainties in the cyanobacterial PSI crystal structure reported at a resolution of 2.5 Å, for which the electron density map has not been reported, the present study suggests that in cyanobacterial PSI, Em(A1A) could be lowered to −718 mV and Em(A1B) to −795 mV when Asp-B575 remained ionized (low-potential A1A form). The Em values in the low-potential A1A form were close to the Em(A1A) = −695 mV and Em(A1B) = −780 mV estimated for Synechocystis sp. PCC 6803 PSI by time-resolved absorption spectroscopy (using Em(FX) = −680 mV and λ = 1.0 eV for forward electron transfer from A1 to FX).14 The Em values in the low-potential A1A form are also close to values listed in old literature reports, particularly for spinach PSI (e.g., Em(A1) = −810 mV12 and −754 mV13). The cyanobacterial PSI crystal structure shows neither the Hbond network nor the water channel that connects Asp-B575 with the protein bulk surface. Indeed, the calculated distribution pattern of water molecules indicated that water molecules were localized only near A1A and A1B (Figure 5). The absence of proton transfer pathways to Asp-B575 implies that Asp-B575 protonation may not be fast enough to occur upon formation of A1A•− in the lifetime of the phyllosemiquinone radical of the forward electron transfer.49 In this case, forward electron transfer from A1A to FX is rapid and does not have enough time to be equilibrated with Asp-B575 protonation, as represented by the refined cyanobacterial PSI structure (i.e., the low-potential A1A form). This implies that the remarkably rapid electron transfer from A0 to A1 has no time to be equilibrated with Asp-B575 protonation in the low-potential A1A form. Cyanobacterial PSI Crystal Structure As the Possible High Potential A1A form. The original geometry of the cyanobacterial PSI crystal structure seems likely to represent the conformation where Asp-B575 is protonated in the presence of A1A•− (high-potential A1A form) (Figure 6). The calculated Em values, Em(A1A) = −612 mV and Em(A1B) = −719 mV (Table 1), were close to the Em(A1A) = −635 mV and Em(A1B) = −690 mV estimated for Synechocystis sp. PCC 6803 PSI by time-resolved absorption spectroscopy (using Em(FX) = −680 mV and λ = 0.7 eV for forward electron transfer from A1 to FX).14
Table 6. Em(A1A) and Em(A1B) Calculated Using the Refined Psi Structure, Where Side-Chain Conformations of Lys-B542 Gln-B678, and Asp-B575 (Including the H-Bonded Water Molecules) Are Modified and QM/MM-Optimized (in mV) A1A
A1B
crystal structure Lys-B542 reoriented Gln-B678 reoriented Asp-B575 ionized Lys-B542 reoriented; Asp-B575 ionized Gln-B678 reoriented; Asp-B575 ionized refined structure
Reoriented or ionized side-chains were QM/MM-optimized. See Supporting Information for the atomic coordinates of the resulting QM region of the refined structure.
DISCUSSION Lower Limit of Em(A1A) and Em(A1B) in the Cyanobacterial PSI Structure. To confirm the identified factors that lowered the calculated Em(A1) for the plant PSI crystal structure with respect to the cyanobacterial PSI crystal structure, we modeled the cyanobacterial PSI crystal structure, where (i) the Lys-B542 side-chain was reoriented to form a saltbridge with Glu-A699 and Asp-B546 (Figure 2a), (ii) the −NH2 and −CO positions of the Gln-B678 side-chain were swapped to form an H-bond with the backbone amide group of Ala-B705 (Figure 3a) as identified in the plant PSI crystal structure, and (iii) the H-bond pattern of the water cluster near A1B was energetically optimized to stabilize the ionized state of Asp-B575 (Figure 6c) (refined cyanobacterial PSI structure). Using the refined cyanobacterial PSI structure, the calculated Em values were significantly lowered to Em(A1A) = −718 mV and Em(A1B) = −795 mV (Table 6), confirming that the
−718 −789 −405 −313 71 −384
A1A
a
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Em refined cyanobacterial PSI structure quinone in uncharged PSI protein volume quinone in water Em shift (water to protein) due to protein charge due to loss of solvation
Em
identified factors were responsible for the majority of the difference in Em calculated for the plant and cyanobacterial crystal structures (Figures 2, 3, and 6). Reorienting the GlnB678 side-chain in the cyanobacterial PSI crystal structure specifically lowered Em(A1B) by ∼60 mV, whereas stabilizing the Asp-B575 ionized state specifically lowered Em(A1A) by ∼70 mV (Table 7). Reorienting only the Lys-B542 side-chain altered neither Em(A1A) nor Em(A1B) significantly because of the induced protonation of Asp-B575. Reorienting the GlnB678 side-chain and stabilizing the Asp-B575 ionized state, without reorienting the Lys-B542 side-chain, resulted in Em(A1A) = −688 mV (Table 7). These results confirm that the significantly lowered values, Em(A1A) = −718 mV and Em(A1B) = −795 mV, for the refined PSI structure could not be obtained without reorienting the Lys-B542 (Figure 2) and GlnG
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Biochemistry As suggested in PSII,50 exposure of PSI crystals to X-rays during crystallographic data collection may cause radical formation and rapid reduction of the redox-active cofactors, leading to accumulation of A1A•−. This might explain why protonated Asp-B575 in the presence of A1A•− is most likely to be the state in the cyanobacterial PSI crystal structure (Figure 6). Notably, in the PSI reaction center, chlorophyll triplets can form upon illumination under reducing conditions.51 Rutherford et al. proposed that protonation of Asp-B575 and formation of the high-potential A1A form could be beneficial under high-light conditions.52 In the high-potential A1A form, the Em difference between A1A and the electron donor A0A is sufficiently large to prevent back-reaction, a trigger of the triplet-generating P•+A0A•− formation. Thus, under conditions where charges accumulate and back-reaction occurs, protonation of Asp-B575 plays a photoprotective role in switching A1A to the high-potential form.52 The replacement of Asp-B575 with Asn in psaB2, a divergent copy of the psaB gene, in the nitrogen-fixing cyanobacterium Nostoc punctiforme,53 implies that the significance of the switchable photoprotective mechanism is less pronounced in the anaerobic conditions encountered during nitrogen fixation, as previously reported.52 The absence of Asp-B575 would increase Em(A1A) and Em(A1B). On the other hand, the rate of electron transfer from A1A•− to FX in PsaB2 might remain unchanged, because mutation of Asp-B575 to Ala and Lys did not significantly affect the rate of electron transfer from A1A•− to FX due to an increase in also Em(FX) in PSI from Synechocystis sp. PCC 6803.18 The localization of all key residues, Asp-B575, Ser-B672, and Trp-B673, in the single protein subunit, PsaB, responsible for the difference between redox potentials of A1A and A1B in both cyanobacterial and plant PSI seems unlikely to be a coincidence. The presence of Trp-B673 locates the carbonyl backbone O atom of Ser-B672 near A1B (Figure 7), specifically lowering Em(A1B) and increasing the A1A•− population. Then, PSI can utilize protonation of Asp-B575 effectively for an increase in Em(A1A), i.e., photoprotection under high-light conditions. Rutherford et al. suggested that the asymmetry existing in PsaA and PsaB, which have not diverged significantly from each other, are likely to be associated with protection and regulation of O2 and heterodimerization of PSI, which occurred after O2 appeared in the environment.52 The ancestral PSI reaction center, which possibly resembles the PsaA/PsaA homodimer,9 might have higher Em(A1A) and Em(A1B) than the more recent PSI (assuming that the other cofactors, e.g., the iron sulfur clusters, are conserved). PsaB might be the subunit that diverged and acquired a photoprotective role in the process of molecular evolution toward current PSI.
Em(A1A) increase of 54 mV in the cyanobacterial PSI structure with respect to the plant PSI structure (Table 2). The −NH2 group of Gln-B678 was unlikely to form a stable H-bond with the backbone-NH group of Ala-B705 in the cyanobacterial PSI crystal structure, whereas the −CO group of Gln-B672 could form a stable H-bond with the backbone −NH group of AlaB699 in the plant PSI crystal structure (Figure 3). The CDloop region (PsaE-40 to 56) in the cyanobacterial PsaE protein subunit is longer than this region in the plant PsaE protein (e.g., refs 45,46). In the plant PSI crystal structure, the lack of the inserted region results in water molecule distributions that shield electrostatic interactions (e.g., the interaction between plant Arg-A697 with A1A; Figure 4). QM/MM-optimized geometries indicate that Asp-B575 was protonated in the presence of A1A•− in the original geometry of the cyanobacterial PSI crystal structure (Figure 6). We demonstrated that even in the cyanobacterial PSI structure, only reorienting the Lys-B542 and Gln-B678 side-chains and rearranging the H-bond pattern of a cluster of water molecules near Asp-B575 significantly decreased the calculated Em values to Em(A1A) = −718 mV and Em(A1B) = −795 mV (refined cyanobacterial PSI structure) (Table 6). Rutherford et al. proposed that protonation of Asp-B575 and formation of the high-potential A1A form could play a photoprotective role in increasing the Em difference between A1A and the electron donor A0A and preventing back-reaction that leads to formation of the triplet-generating P•+A0A•− intermediate state.52 The original geometry of the cyanobacterial PSI crystal structure might represent the high-potential A1A form, whereas the refined cyanobacterial PSI structure might resemble the low-potential A1A form. Three residues in PsaB, cyanobacterial Asp-B575, Ser-B672, and Trp-B673 (plant Asp-B569, Ser-B666, and Trp-B667), were largely responsible for the difference between Em(A1A) and Em(A1B).16 The bulky Trp-B673 side-chain makes the backbone carbonyl O atom of Ser-B672 orient toward A1B, lowering Em(A1B) with respect to Em(A1A) (Figure 7). Intriguingly, these three residues belong specifically to PsaB. PsaB might have diverged from PsaA and acquired a photoprotective role after O2 appeared in the environment.52
CONCLUDING REMARKS Em(A1A) and Em(A1B) were calculated to be −773 and −818 mV, respectively, for the plant PSI crystal structure and −612 and −719 mV, respectively, for the cyanobacterial PSI crystal structure (Table 1). The difference in the side-chain orientation between cyanobacterial Lys-B542 and Gln-B678 and plant LysB536 and Gln-B672 and the associated protonation state of cyanobacterial Asp-B575/plant Asp-B569 were largely responsible for the Em(A1) difference between the cyanobacterial and plant PSI crystal structures. The crystal structures show that cyanobacterial Lys-B542 is oriented toward A1A, whereas plant Lys-B536 is oriented away from A1A and is stabilized by saltbridges with Glu-A702 and Asp-B540 (Figure 2). The difference in the Lys side-chain orientation results in an
Atomic charges; QM/MM-optimized atomic coordinates (PDF) Protein database file (PDB)
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ASSOCIATED CONTENT
S Supporting Information *
The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.biochem.7b00082.
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AUTHOR INFORMATION
Corresponding Author
*Tel. +81-3-5452-5056. Fax: +81-3-5452-5083. E-mail: hiro@ appchem.t.u-tokyo.ac.jp. ORCID
Hiroshi Ishikita: 0000-0002-5849-8150 Notes
The authors declare no competing financial interest. H
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ACKNOWLEDGMENTS This research was supported by JST CREST (JPMJCR1656), JSPS KAKENHI (JP15H00864, JP16H06560, JP26105012, and JP26711008), Japan Agency for Medical Research and Development (AMED), Materials Integration for engineering polymers of Cross-ministerial Strategic Innovation Promotion Program (SIP), and Interdisciplinary Computational Science Program in CCS, University of Tsukuba. Theoretical calculations were partly performed using Research Center for Computational Science, Okazaki, Japan.
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DOI: 10.1021/acs.biochem.7b00082 Biochemistry XXXX, XXX, XXX−XXX
