Mechanism of proton-coupled quinone reduction in Photosystem II

Cryo-electron microscopy reveals hydrogen positions and water networks in photosystem II

Photosystem II starts the photosynthetic electron transport chain that converts solar energy into chemical energy and thus sustains life on Earth. It catalyzes two chemical reactions: water oxidation to molecular oxygen and plastoquinone reduction. Coupling of electron and proton transfer is crucial for efficiency; however, the molecular basis of these processes remains speculative owing to uncertain water binding sites and the lack of experimentally determined hydrogen positions. We thus collected high-resolution cryo-electron microscopy data of fully hydrated photosystem II from the thermophilic cyanobacterium Thermosynechococcus vestitus to a final resolution of 1.71 angstroms. The structure reveals several previously undetected partially occupied water binding sites and more than half of the hydrogen and proton positions. This clarifies the pathways of substrate water binding and plastoquinone B protonation.

Energetics of the H-Bond Network in Exiguobacterium sibiricum Rhodopsin

Exiguobacterium sibiricum rhodopsin (ESR) functions as a light-driven proton pump utilizing Lys96 for proton uptake and maintaining its activity over a wide pH range. Using a combination of methodologies including the linear Poisson-Boltzmann equation and a quantum mechanical/molecular mechanical approach with a polarizable continuum model, we explore the microscopic mechanisms underlying its pumping activity. Lys96, the primary proton uptake site, remains deprotonated owing to the loss of solvation in the ESR protein environment. Asp85, serving as a proton acceptor group for Lys96, does not form a low-barrier H-bond with His57. Instead, deprotonated Asp85 forms a salt-bridge with protonated His57, and the proton is predominantly located at the His57 moiety. Glu214, the only acidic residue at the end of the H-bond network exhibits a pKa value of ∼6, slightly elevated due to solvation loss. It seems likely that the H-bond network [Asp85···His57···H2O···Glu214] serves as a proton-conducting pathway toward the protein bulk surface.

Iron mobilization from intact ferritin: effect of differential redox activity of quinone derivatives with NADH/O2 and in situ-generated ROS

Ferritins are multimeric nanocage proteins that sequester/concentrate excess of free iron and catalytically synthesize a hydrated ferric oxyhydroxide bio-mineral. Besides functioning as the primary intracellular iron storehouses, these supramolecular assemblies also oversee the controlled release of iron to meet physiologic demands. By virtue of the reducing nature of the cytosol, reductive dissolution of ferritin-iron bio-mineral by physiologic reducing agents might be a probable pathway operating in vivo. Herein, to explore this reductive iron-release pathway, a series of quinone analogs differing in size, position/nature of substituents and redox potentials were employed to relay electrons from physiologic reducing agent, NADH, to the ferritin core. Quinones are well known natural electron/proton mediators capable of facilitating both 1/2 electron transfer processes and have been implicated in iron/nutrient acquisition in plants and energy transduction. Our findings on the structure-reactivity of quinone mediators highlight that iron release from ferritin is dictated by electron-relay capability (dependent on E1/2 values) of quinones, their molecular structure (i.e., the presence of iron-chelation sites and the propensity for H-bonding) and the type/amount of reactive oxygen species (ROS) they generate in situ. Juglone/Plumbagin released maximum iron due to their intermediate E1/2 values, presence of iron chelation sites, the ability to inhibit in situ generation of H2O2 and form intramolecular H-bonding (possibly promotes semiquinone formation). This study may strengthen our understanding of the ferritin-iron-release process and their significance in bioenergetics/O2-based cellular metabolism/toxicity while providing insights on microbial/plant iron acquisition and the dynamic host-pathogen interactions.

Exploring the Deprotonation Process during Incorporation of a Ligand Water Molecule at the Dangling Mn Site in Photosystem II

The Mn4CaO5 cluster, featuring four ligand water molecules (W1 to W4), serves as the water-splitting site in photosystem II (PSII). X-ray free electron laser (XFEL) structures exhibit an additional oxygen site (O6) adjacent to the O5 site in the fourth lowest oxidation state, S3, forming Mn4CaO6. Here, we investigate the mechanism of the second water ligand molecule at the dangling Mn (W2) as a potential incorporating species, using a quantum mechanical/molecular mechanical (QM/MM) approach. Previous QM/MM calculations demonstrated that W1 releases two protons through a low-barrier H-bond toward D1-Asp61 and subsequently releases an electron during the S2 to S3 transition, resulting in O•- at W1 and protonated D1-Asp61. During the process of Mn4CaO6 formation, O•-, rather than H2O or OH-, best reproduced the O5···O6 distance. Although the catalytic cluster with O•- at O6 is more stable than that with O•- at W1 in S3, it does not occur spontaneously due to the significantly uphill deprotonation process. Assuming O•- at W2 incorporates into the O6 site, an exergonic conversion from Mn1(III)Mn2(IV)Mn3(IV)Mn4(IV) (equivalent to the open-cubane S2 valence state) to Mn1(IV)Mn2(IV)Mn3(IV)Mn4(III) (equivalent to the closed-cubane S2 valence state) occurs. These findings provide energetic insights into the deprotonation and structural conversion events required for the Mn4CaO6 formation.

Mutagenesis of Ile184 in the cd-loop of the photosystem II D1 protein modifies acceptor-side function via spontaneous mutation of D1-His252 in Synechocystis sp. PCC 6803

The Photosystem II water-plastoquinone oxidoreductase is a multi-subunit complex which catalyses the light-driven oxidation of water to molecular oxygen in oxygenic photosynthesis. The D1 reaction centre protein exists in multiple forms in cyanobacteria, including D1FR which is expressed under far-red light. We investigated the role of Phe184 that is found in the lumenal cd-loop of D1FR but is typically an isoleucine in other D1 isoforms. The I184F mutant in Synechocystis sp. PCC 6803 was similar to the control strain but accumulated a spontaneous mutation that introduced a Gln residue in place of His252 located on the opposite side of the thylakoid membrane. His252 participates in the protonation of the secondary plastoquinone electron acceptor QB. The I184F:H252Q double mutant exhibited reduced high-light-induced photodamage and an altered QB-binding site that impaired herbicide binding. Additionally, the H252Q mutant had a large increase in the variable fluorescence yield although the number of photochemically active PS II centres was unchanged. In the I184F:H252Q mutant the extent of the increased fluorescence yield decreased. Our data indicates substitution of Ile184 to Phe modulates PS II-specific variable fluorescence in cells with the His252 to Gln substitution by modifying the QB-binding site.

Rotaxane-Functionalized Dyes for Charge-Rectification in p-Type Photoelectrochemical Devices

A supramolecular photovoltaic strategy is applied to enhance power conversion efficiencies (PCE) of photoelectrochemical devices by suppressing electron-hole recombination after photoinduced electron transfer (PET). Here, the author exploit supramolecular localization of the redox mediator-in close proximity to the dye-through a rotaxane topology, reducing electron-hole recombination in p-type dye-sensitized solar cells (p-DSSCs). Dye PRotaxane features 1,5-dioxynaphthalene recognition sites (DNP-arms) with a mechanically-interlocked macrocyclic redox mediator naphthalene diimide macrocycle (3-NDI-ring), stoppering synthetically via click chemistry. The control molecule PStopper has stoppered DNP-arms, preventing rotaxane formation with the 3-NDI-ring. Transient absorption and time-resolved fluorescence spectroscopy studies show ultrafast (211 ± 7 fs and 2.92 ± 0.05 ps) PET from the dye-moiety of PRotaxane to its mechanically interlocked 3-NDI-ring-acceptor, slowing down the electron-hole recombination on NiO surfaces compared to the analogue . p-DSSCs employing PRotaxane (PCE = 0.07%) demonstrate a 30% PCE increase compared to PStopper (PCE = 0.05%) devices, combining enhancements in both open-circuit voltages (VOC = 0.43 vs 0.36 V) and short-circuit photocurrent density (JSC = -0.39 vs -0.34 mA cm-2 ). Electrochemical impedance spectroscopy shows that PRotaxane devices exhibit hole lifetimes (τh ) approaching 1 s, a 16-fold improvement compared to traditional I- /I3 - -based systems (τh = 50 ms), demonstrating the benefits obtained upon nanoengineering of interfacial dye-regeneration at the photocathode.

Role of hydrogen-bond networks on the donor side of photosynthetic reaction centers from purple bacteria

For the last decades, significant progress has been made in studying the biological functions of H-bond networks in membrane proteins, proton transporters, receptors, and photosynthetic reaction centers. Increasing availability of the X-ray crystal and cryo-electron microscopy structures of photosynthetic complexes resolved with high atomic resolution provides a platform for their comparative analysis. It allows identifying structural factors that are ensuring the high quantum yield of the photochemical reactions and are responsible for the stability of the membrane complexes. The H-bond networks are known to be responsible for proton transport associated with electron transfer from the primary to the secondary quinone as well as in the processes of water oxidation in photosystem II. Participation of such networks in reactions proceeding on the periplasmic side of bacterial photosynthetic reaction centers is less studied. This review summarizes the current understanding of the role of H-bond networks on the donor side of photosynthetic reaction centers from purple bacteria. It is discussed that the networks may be involved in providing close association with mobile electron carriers, in light-induced proton transport, in regulation of the redox properties of bacteriochlorophyll cofactors, and in stabilization of the membrane protein structure at the interface of membrane and soluble phases.

New insights into the proton pumping mechanism of ba3 cytochrome c oxidase: the functions of key residues and water

As the terminal oxidase of cell respiration in mitochondria and aerobic bacteria, the proton pumping mechanism of ba3-type cytochrome c oxidase (CcO) of Thermus thermophiles is still not fully understood. Especially, the functions of key residues which were considered as the possible proton loading sites (PLSs) above the catalytic center, as well as water located above and within the catalytic center, remain unclear. In this work, molecular dynamic simulations were performed on a set of designed mutants of key residues (Asp287, Asp372, His376, and Glu126II). The results showed that Asp287 may not be a PLS, but it could modulate the ability of the proton transfer pathway to transfer protons through its salt bridge with Arg225. Maintaining the closed state of the water pool above the catalytic center is necessary for the participation of inside water molecules in proton transfer. Water molecules inside the water pool can form hydrogen bond chains with PLS to facilitate proton transfer. Additional quantum cluster models of the Fe-Cu metal catalytic center are established, indicating that when the proton is transferred from Tyr237, it is more likely to reach the OCu atom directly through only one water molecule. This work provides a more profound understanding of the functions of important residues and specific water molecules in the proton pumping mechanism of CcO.

Lys264 of the D2 Protein Performs a Dual Role in Photosystem II Modifying Assembly and Electron Transfer through the Quinone-Iron Acceptor Complex

Bicarbonate (HCO3-) binding regulates electron flow between the primary (QA) and secondary (QB) plastoquinone electron acceptors of Photosystem II (PS II). Lys264 of the D2 subunit of PS II contributes to a hydrogen-bond network that stabilizes HCO3- ligation to the non-heme iron in the QA-Fe-QB complex. Using the cyanobacterium Synechocystis sp. PCC 6803, alanine and glutamate were introduced to create the K264A and K264E mutants. Photoautotrophic growth was slowed in K264E cells but not in the K264A strain. Both mutants accumulated an unassembled CP43 precomplex as well as the CP43-lacking RC47 assembly intermediate, indicating weakened binding of the CP43 precomplex to RC47. Assembly was impeded more in K264E cells than in the K264A strain, but K264A cells were more susceptible to high-light-induced photodamage when assayed using PS II-specific electron acceptors. Furthermore, an impaired repair mechanism was observed in the K264A mutant in protein labeling experiments. Unexpectedly, unlike the K264A strain, the K264E mutant displayed inhibited oxygen evolution following high-light exposure when HCO3- was added to support whole chain electron transport. In both mutants, the decay of chlorophyll fluorescence was slowed, indicating impaired electron transfer between QA and QB. Furthermore, the fluorescence decay kinetics in the K264E strain were insensitive to addition of either formate or HCO3-, whereas HCO3--reversible formate-induced inhibition in the K264A mutant was observed. Exchange of plastoquinol with the membrane plastoquinone pool at the QB-binding site was also retarded in both mutants. Hence, D2-Lys264 possesses key roles in both assembly and activity of PS II.

Solvent-switchable regioselective 1,2- or 1,6-addition of quinones with boronic acids

An efficient copper-catalyzed solvent-switchable regioselective 1,2- or 1,6-addition of quinones with boronic acids has been developed. This novel catalytic protocol for the synthesis of various quinols and 4-phenoxyphenols was enabled by a simple solvent swap between H₂O and MeOH. It features mild reaction conditions, simple and easy operation, broad substrate scope and excellent regioselectivity. The gram-scale reactions as well as the further transformations of both addition products were also successfully investigated.

Structural insights into the action mechanisms of artificial electron acceptors in photosystem II

Photosystem II (PSII) utilizes light energy to split water, and the electrons extracted from water are transferred to Q_B, a plastoquinone (PQ) molecule bound to the D1 subunit of PSII. Many artificial electron acceptors (AEAs) with similar molecular structures to PQ can accept electrons from PSII. However, the molecular mechanism by which AEAs act on PSII is unclear. Here, we solved the crystal structure of PSII treated with three different AEAs, 2,5-dibromo-1,4-benzoquinone, 2,6-dichloro-1,4-benzoquinone, and 2-phenyl-1,4-benzoquinone, at 1.95-2.10 Å resolution. Our results show that all AEAs substitute for Q_B and are bound to the Q_B-binding site (Q_B site) to receive electrons, but their binding strengths are different, resulting in differences in their efficiencies to accept electrons. The acceptor 2-phenyl-1,4-benzoquinone binds most weakly to the Q_B site, and showed the highest oxygen-evolving activity, implying a reverse relationship between the binding strength and oxygen-evolving activity. In addition, a novel quinone binding site, designated the Q_D site, was discovered, which is located in the vicinity of Q_B site and close to Q_C site, a binding site reported previously. This Q_D site is expected to play a role as a channel or a storage site for quinones to be transported to the Q_B site. These results provide the structural basis for elucidating the actions of AEAs and exchange mechanism of Q_B in PSII, and also provide information for the design of more efficient electron acceptors.

Mechanism of Asparagine-Mediated Proton Transfer in Photosynthetic Reaction Centers

In photosynthetic reaction centers from purple bacteria (PbRCs), light-induced charge separation leads to the reduction of the terminal electron acceptor quinone, QB. The reduction of QB to QB•- is followed by protonation via Asp-L213 and Ser-L223 in PbRC from Rhodobacter sphaeroides. However, Asp-L213 is replaced with nontitratable Asn-L222 and Asn-L213 in PbRCs from Thermochromatium tepidum and Blastochloris viridis, respectively. Here, we investigated the energetics of proton transfer along the asparagine-involved H-bond network using a quantum mechanical/molecular mechanical approach. The potential energy profile for the H-bond between H3O+ and the carbonyl O site of Asn-L222 shows that the proton is predominantly localized at the Asn-L222 moiety in the T. tepidum PbRC protein environment, easily forming the enol species. The release of the proton from the amide -NH2 site toward Ser-L232 via tautomerization suffers from the energy barrier. Upon reorientation of Asn-L222, the enol -OH site forms a short low-barrier H-bond with Ser-L232, facilitating protonation of QB•- in a Grotthuss-like mechanism. This is a basis of how asparagine or glutamine side chains function as acceptors/donors in proton transfer pathways.

Photocatalytic CO2 reduction with aminoanthraquinone organic dyes

The direct utilization of solar energy to convert CO₂ into renewable chemicals remains a challenge. One essential difficulty is the development of efficient and inexpensive light-absorbers. Here we show a series of aminoanthraquinone organic dyes to promote the efficiency for visible light-driven CO₂ reduction to CO when coupled with an Fe porphyrin catalyst. Importantly, high turnover numbers can be obtained for both the photosensitizer and the catalyst, which has not been achieved in current light-driven systems. Structure-function study performed with substituents having distinct electronic effects reveals that the built-in donor-acceptor property of the photosensitizer significantly promotes the photocatalytic activity. We anticipate this study gives insight into the continued development of advanced photocatalysts for solar energy conversion.

Functional Water Networks in Fully Hydrated Photosystem II

Water channels and networks within photosystem II (PSII) of oxygenic photosynthesis are critical for enzyme structure and function. They control substrate delivery to the oxygen-evolving center and mediate proton transfer at both the oxidative and reductive endpoints. Current views on PSII hydration are derived from protein crystallography, but structural information may be compromised by sample dehydration and technical limitations. Here, we simulate the physiological hydration structure of a cyanobacterial PSII model following a thorough hydration procedure and large-scale unconstrained all-atom molecular dynamics enabled by massively parallel simulations. We show that crystallographic models of PSII are moderately to severely dehydrated and that this problem is particularly acute for models derived from X-ray free electron laser (XFEL) serial femtosecond crystallography. We present a fully hydrated representation of cyanobacterial PSII and map all water channels, both static and dynamic, associated with the electron donor and acceptor sides. Among them, we describe a series of transient channels and the attendant conformational gating role of protein components. On the acceptor side, we characterize a channel system that is absent from existing crystallographic models but is likely functionally important for the reduction of the terminal electron acceptor plastoquinone Q_B. The results of the present work build a foundation for properly (re)evaluating crystallographic models and for eliciting new insights into PSII structure and function.

Electron Transfer Route between Quinones in Type-II Reaction Centers

In photosynthetic reaction centers from purple bacteria (PbRCs) and photosystem II (PSII), the photoinduced charge separation is terminated by an electron transfer between the primary (QA) and secondary (QB) quinones. Here, we investigate the electron transfer route, calculating the superexchange coupling (HQA-QB) for electron transfer from QA to QB in the protein environment. HQA-QB is significantly larger in PbRC than in PSII. In superexchange electron tunneling, the electron transfer via unoccupied molecular orbitals of the nonheme Fe complex (QA → Fe → QB) is pronounced in PbRC, whereas the electron transfer via occupied molecular orbitals (Fe → QB followed by QA → Fe) is pronounced in PSII. The significantly large HQA-QB is caused by a water molecule that donates the H-bond to the ligand Glu-M234 in PbRC. The corresponding water molecule is absent in PSII due to the existence of D1-Tyr246. HQA-QB increases in response to the Ser-L223···QB H-bond formation caused by an extension of the H-bond network, which facilitates charge delocalization over the QB site. This explains the observed discrepancy in the QA-to-QB electron transfer between PbRC and PSII, despite their structural similarity.

Proton-mediated photoprotection mechanism in photosystem II

Photo-induced charge separation, which is terminated by electron transfer from the primary quinone Q_A to the secondary quinone Q_B, provides the driving force for O₂ evolution in photosystem II (PSII). However, the backward charge recombination using the same electron-transfer pathway leads to the triplet chlorophyll formation, generating harmful singlet-oxygen species. Here, we investigated the molecular mechanism of proton-mediated Q_A ^⋅- stabilization. Quantum mechanical/molecular mechanical (QM/MM) calculations show that in response to the loss of the bicarbonate ligand, a low-barrier H-bond forms between D2-His214 and Q_A ^⋅-. The migration of the proton from D2-His214 toward Q_A ^⋅- stabilizes Q_A ^⋅-. The release of the bicarbonate ligand from the binding Fe²⁺ site is an energetically uphill process, whereas the bidentate-to-monodentate reorientation is almost isoenergetic. These suggest that the bicarbonate protonation and decomposition may be a basis of the mechanism of photoprotection via Q_A ^⋅-/Q_AH^⋅ stabilization, increasing the Q_A redox potential and activating a charge-recombination pathway that does not generate the harmful singlet oxygen.

Conformational Changes and H-Bond Rearrangements during Quinone Release in Photosystem II

In photosystem II (PSII) and photosynthetic reaction centers from purple bacteria (PbRC), the electron released from the electronically excited chlorophyll is transferred to the terminal electron acceptor quinone, Q_B. Q_B accepts two electrons and two protons before leaving the protein. We investigated the molecular mechanism of quinone exchange in PSII, conducting molecular dynamics (MD) simulations and quantum mechanical/molecular mechanical (QM/MM) calculations. MD simulations suggest that the release of Q_B leads to the transformation of the short helix (D1-Phe260 to D1-Ser264), which is adjacent to the stromal helix de (D1-Asn247 to D1-Ile259), into a loop and to the formation of a water-intake channel. Water molecules enter the Q_B binding pocket via the channel and form an H-bond network. QM/MM calculations indicate that the H-bond network serves as a proton-transfer pathway for the reprotonation of D1-His215, the proton donor during Q_BH^-/Q_BH₂ conversion. Together with the absence of the corresponding short helix but the presence of Glu-L212 in PbRC, it seems likely that the two type-II reaction centers undergo quinone exchange via different mechanisms.

Tyr244 of the D2 Protein Is Required for Correct Assembly and Operation of the Quinone-Iron-Bicarbonate Acceptor Complex of Photosystem II

Two plastoquinone electron acceptors, Q_A and Q_B, are present in Photosystem II (PS II) with their binding sites formed by the D2 and D1 proteins, respectively. A hexacoordinate non-heme iron is bound between Q_A and Q_B by D2 and D1, each providing two histidine ligands, and a bicarbonate that is stabilized via hydrogen bonds with D2-Tyr244 and D1-Tyr246. Both tyrosines and bicarbonate are conserved in oxygenic photosynthetic organisms but absent from the corresponding quinone-iron electron acceptor complex of anoxygenic photosynthetic bacteria. We investigated the role of D2-Tyr244 by introducing mutations in the cyanobacterium Synechocystis sp. PCC 6803. Alanine, histidine, and phenylalanine substitutions were introduced creating the Y244A, Y244H, and Y244F mutants. Electron transfer between Q_A and Q_B was impaired, the back-reaction with the S2 state of the oxygen-evolving complex was modified, and PS II assembly was disrupted, with the Y244A strain being more affected than the Y244F and Y244H mutants. The strains were also highly susceptible to photodamage in the presence of PS II-specific electron acceptors. Thermoluminescence and chlorophyll a fluorescence decay measurements indicated that the redox potential of the Q_A/Q_A^- couple became more positive in the Y244F and Y244H mutants, consistent with bicarbonate binding being impacted. The replacement of Tyr244 by alanine also led to an insertion of two amino acid repeats from Gln239 to Ala249 within the DE loop of D2, resulting in an inactive PS II complex that lacked PS II-specific variable fluorescence. The 66 bp insertion giving rise to the inserted amino acids therefore created an obligate photoheterotrophic mutant.

pH-Dependent Regulation of Electron Flow in Photosystem II by a Histidine Residue at the Stromal Surface

In photosystem II (PSII), the secondary plastoquinone electron acceptor Q_B functions as a substrate that converts into plastoquinol upon its double reduction by electrons abstracted from water. It has been suggested that a histidine residue, D1-H252, which is located at the stromal surface near Q_B, is involved in the pH-dependent regulation of electron flow and proton transfer to Q_B. However, definitive evidence for the involvement of D1-H252 in the Q_B reactions has not been obtained yet. Here, we studied the roles of D1-H252 in PSII using a cyanobacterial mutant, in which D1-H252 was replaced with Ala. Delayed luminescence (DL) measurement upon a single flash showed a faster Q_B^- decay at higher pH in the thylakoids from the wild-type strain due to the downshift of the redox potential of Q_B [E_m(Q_B^-/Q_B)]. This pH dependence of the Q_B^- decay was lost in the D1-H252A mutant. The experimental E_m(Q_B^-/Q_B) changes were well reproduced by the density functional theory calculations for models with different protonation states of D1-H252 and with Ala replaced for H252. It was further shown that the period-four oscillation of the DL intensity by successive flashes was significantly diminished in the D1-H252A mutant, suggesting the inhibition of plastoquinone exchange at the Q_B pocket in this mutant. It is thus concluded that D1-H252 is a key amino acid residue that regulates electron flow in PSII by sensing pH in the stroma and stabilizes the Q_B binding site to facilitate the quinone exchange reaction.

Release of a Proton and Formation of a Low-Barrier Hydrogen Bond between Tyrosine D and D2-His189 in Photosystem II

In photosystem II (PSII), the second-lowest oxidation state (S₁) of the oxygen-evolving Mn₄CaO₅ cluster is the most stable, as the radical form of the redox-active D2-Tyr160 is considered to be a candidate that accepts an electron from the lowest oxidation state (S₀) in the dark. Using quantum mechanical/molecular mechanical calculations, we investigated the redox potential (E _m) of TyrD and its H-bond partner, D2-His189. The potential energy profile indicates that the release of a proton from the TyrD...D2-His189 pair leads to the formation of a low-barrier H-bond. The E _m depends on the H⁺ position along the low-barrier H-bond, e.g., 680 mV when the H⁺ is at the D2-His189 moiety and 800 mV when the H⁺ is at the TyrD moiety, which can explain why TyrD mediates both the S₀ to S₁ oxidation and the S₂ to S₁ reduction.

Absorption wavelength along chromophore low-barrier hydrogen bonds

In low-barrier hydrogen bonds (H-bonds), the pK_a values for the H-bond donor and acceptor moieties are nearly equal, whereas the redox potential values depend on the H⁺ position. Spectroscopic details of low-barrier H-bonds remain unclear. Here, we report the absorption wavelength along low-barrier H-bonds in protein environments, using a quantum mechanical/molecular mechanical approach. Low-barrier H-bonds form between Glu46 and p-coumaric acid (pCA) in the intermediate pR_CW state of photoactive yellow protein and between Asp116 and the retinal Schiff base in the intermediate M-state of the sodium-pumping rhodopsin KR2. The H⁺ displacement of only ∼0.4 Å, which does not easily occur without low-barrier H-bonds, is responsible for the ∼50 nm-shift in the absorption wavelength. This may be a basis of how photoreceptor proteins have evolved to proceed photocycles using abundant protons.

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The low-barrier H-bond formation is a prerequisite for proton transfer

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How the absorption wavelength changes as H⁺ moves is an open question

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The H⁺ displacement of ∼0.4 Å leads to the absorption wavelength shift of ∼50 nm

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The localization of the molecular orbitals plays a key role in the wavelength shift

Redox properties and regulatory mechanism of the iron-quinone electron acceptor in photosystem II as revealed by FTIR spectroelectrochemistry

Photosystem II (PSII) performs oxidation of water and reduction of plastoquinone through light-induced electron transfer. Electron transfer reactions at individual redox cofactors are controlled by their redox potentials, and the forward and backward electron flows in PSII are regulated by tuning them. It is, thus, crucial to accurately estimate the redox potentials of the cofactors and their shifts by environmental changes to understand the regulatory mechanisms in PSII. Fourier-transform infrared (FTIR) spectroelectrochemistry combined with a light-induced difference technique is a powerful method to investigate the mechanisms of the redox reactions in PSII. In this review, we introduce the methodology and the application of this method in the studies of the iron-quinone complex, which consists of two plastoquinone molecules, Q_A and Q_B, and the non-heme iron, on the electron-acceptor side of PSII. It is shown that FTIR spectroelectrochemistry is a useful method not only for estimating the redox potentials but also for detecting the reactions of nearby amino-acid residues coupled with the redox reactions.

Comparison of proton transfer paths to the QA and QB sites of the Rb. sphaeroides photosynthetic reaction centers

The photosynthetic bacterial reaction centers from purple non-sulfur bacteria use light energy to drive the transfer of electrons from cytochrome c to ubiquinone. Ubiquinone bound in the Q_A site cycles between quinone, Q_A, and anionic semiquinone, Q_A^·-, being reduced once and never binding protons. In the Q_B site, ubiquinone is reduced twice by Q_A^·-, binds two protons and is released into the membrane as the quinol, QH₂. The network of hydrogen bonds formed in a molecular dynamics trajectory was drawn to investigate proton transfer pathways from the cytoplasm to each quinone binding site. Q_A is isolated with no path for protons to enter from the surface. In contrast, there is a complex and tangled network requiring residues and waters that can bring protons to Q_B. There are three entries from clusters of surface residues centered around HisH126, GluH224, and HisH68. The network is in good agreement with earlier studies, Mutation of key nodes in the network, such as SerL223, were previously shown to slow proton delivery. Mutational studies had also shown that double mutations of residues such as AspM17 and AspL210 along multiple paths in the network presented here slow the reaction, while single mutations do not. Likewise, mutation of both HisH126 and HisH128, which are at the entry to two paths reduce the rate of proton uptake.

Review on NAD(P)H dehydrogenase quinone 1 (NQO1) pathway

NQO1 is an enzyme present in humans which is encoded by NQO1 gene. It is a protective antioxidant agent, versatile cytoprotective agent and regulates the oxidative stresses of chromatin binding proteins for DNA damage in cancer cells. The oxidization of cellular pyridine nucleotides causes structural alterations to NQO1 and changes in its capacity to binding of proteins. A strategy based on NQO1 to have protective effect against cancer was developed by organic components to enhance NQO1 expression. The quinone derivative compounds like mitomycin C, RH1, E09 (Apaziquone) and β-lapachone causes cell death by NQO1 reduction of two electrons. It was also known to be overexpressed in various tumor cells of breast, lung, cervix, pancreas and colon when it was compared with normal cells in humans. The mechanism of NQO1 by the reduction of FAD by NADPH to form FADH2 is by two ways to inhibit cancer cell development such as suppression of carcinogenic metabolic activation and prevention of carcinogen formation. The NQO1 exhibit suppression of chemical-mediated carcinogenesis by various properties of NQO1 which includes, detoxification of quinone scavenger of superoxide anion radical, antioxidant enzyme, protein stabilizer. This review outlines the NQO1 structure, mechanism of action to inhibit the cancer cell, functions of NQO1 against oxidative stress, drugs acting on NQO1 pathways, clinical significance.

Experimental and calculated infrared spectra of disubstituted naphthoquinones

In recent years there has been interest in incorporating substituted 1,4-naphthoquinones (NQs) into the A₁ binding site in photosystem I (PSI) photosynthetic protein complexes. This interest in part stems from the considerably altered bioenergetics of electron transfer that occur in PSI with such substitutions. Time resolved FTIR studies of PSI complexes with disubstituted NQs incorporated have and currently are being undertaken, and with this in mind it is worth considering FTIR absorption spectra of these disubstituted NQs in solution. Here we present FTIR absorbance spectra for 2-bromo-3-methyl-1,4-naphthoquinone (BrMeNQ), 2-chloromethyl-3-methyl-1,4-naphthoquinone (CMMeNQ) and 2-ethylthio-3-methyl-1,4-naphthoquinone (ETMeNQ) in tetrahydrofuran (THF). The FTIR spectra of these di-substituted naphthoquinones (NQs) were compared to FTIR spectra of 2-methyl-3-phytyl-1,4-naphthoquinone [phylloquinone (PhQ)], 2,3-dimethyl-1,4-naphthoquinone (DMNQ), and 2-methyl-1,4-naphthoquinone (2MNQ). To aid in the assignment of bands in the experimental spectra, density functional theory (DFT) based vibrational frequency calculations for all the substituted NQs in solution were undertaken. The calculated and experimental spectra agree well. By calculating normal mode potential energy distributions, unambiguous quantitative band assignments were made. The calculated and experimental spectra together make predictions about what may be observable in time resolved FTIR difference spectra obtained using PSI with the different NQs incorporated. Time resolved FTIR difference spectra are presented that support these predictions.

Ultrafast transient absorption spectroelectrochemistry: femtosecond to nanosecond excited-state relaxation dynamics of the individual components of an anthraquinone redox couple

Many photoactivated processes involve a change in oxidation state during the reaction pathway and formation of highly reactive photoactivated species. Isolating these reactive species and studying their early-stage femtosecond to nanosecond (fs-ns) photodynamics can be challenging. Here we introduce a combined ultrafast transient absorption-spectroelectrochemistry (TA-SEC) approach using freestanding boron doped diamond (BDD) mesh electrodes, which also extends the time domain of conventional spectrochemical measurements. The BDD electrodes offer a wide solvent window, low background currents, and a tuneable mesh size which minimises light scattering from the electrode itself. Importantly, reactive intermediates are generated electrochemically, via oxidation/reduction of the starting stable species, enabling their dynamic interrogation using ultrafast TA-SEC, through which the early stages of the photoinduced relaxation mechanisms are elucidated. As a model system, we investigate the ultrafast spectroscopy of both anthraquinone-2-sulfonate (AQS) and its less stable counterpart, anthrahydroquinone-2-sulfonate (AH2QS). This is achieved by generating AH2QS in situ from AQS via electrochemical means, whilst simultaneously probing the associated early-stage photoinduced dynamical processes. Using this approach we unravel the relaxation mechanisms occurring in the first 2.5 ns, following absorption of ultraviolet radiation; for AQS as an extension to previous studies, and for the first time for AH2QS. AQS relaxation occurs via formation of triplet states, with some of these states interacting with the buffered solution to form a transient species within approximately 600 ps. In contrast, all AH2QS undergoes excited-state single proton transfer with the buffered solution, resulting in formation of ground state AHQS- within approximately 150 ps.

Nitric oxide represses photosystem II and NDH-1 in the cyanobacterium Synechocystis sp. PCC 6803

Photosynthetic electron transfer comprises a series of light-induced redox reactions catalysed by multiprotein machinery in the thylakoid. These protein complexes possess cofactors susceptible to redox modifications by reactive small molecules. The gaseous radical nitric oxide (NO), a key signalling molecule in green algae and plants, has earlier been shown to bind to Photosystem (PS) II and obstruct electron transfer in plants. The effects of NO on cyanobacterial bioenergetics however, have long remained obscure. In this study, we exposed the model cyanobacterium Synechocystis sp. PCC 6803 to NO under anoxic conditions and followed changes in whole-cell fluorescence and oxidoreduction of P700 in vivo. Our results demonstrate that NO blocks photosynthetic electron transfer in cells by repressing PSII, PSI, and likely the NDH dehydrogenase-like complex 1 (NDH-1). We propose that iron‑sulfur clusters of NDH-1 complex may be affected by NO to such an extent that ferredoxin-derived electron injection to the plastoquinone pool, and thus cyclic electron transfer, may be inhibited. These findings reveal the profound effects of NO on Synechocystis cells and demonstrate the importance of controlled NO homeostasis in cyanobacteria.

Long-Range Electron Tunneling from the Primary to Secondary Quinones in Photosystem II Enhanced by Hydrogen Bonds with a Nonheme Fe Complex

The mechanisms governing the long-range electron tunneling from the primary (Q_A) to secondary (Q_B) quinones in photosystem II are clarified by analyzing superexchange pathways through a nonheme Fe complex, using a quantum mechanics/molecular mechanics/polarizable continuum model approach. The electron tunneling rate is evaluated using the Marcus-Levich-Jortner theory considering electronic coupling, energy difference, and Franck-Condon factor. The superexchange Q_A → Q_B electron tunneling is enhanced by hybridized σ/σ* orbitals of histidines (D2-His214 and D1-His215) via penetration of the wave function into hydrogen bonds with both Q_A and Q_B. Despite a large energy gap to the intermediate states, the contributions of the histidine σ/σ* orbitals to the superexchange coupling are larger than those of π/π* orbitals. Fe²⁺ is not an essential component for the Q_A → Q_B electron tunneling because hybridized histidine molecular orbitals can be coupled with both Q_A and Q_B simultaneously in the absence of Fe d orbitals.

The Interaction of Water-Soluble Nitroxide Radicals with Photosystem II

In this work, we investigated the redox transients of a number of water-soluble spin labels upon their interactions with Photosystem II (PS II) core complexes isolated from spinach leaves. We have found that the reactivity of nitroxide radicals, determined by the rate of their reduction upon illumination of PS II, depends on the chemical structure of radicals and the capability of their coming close to low-potential redox centers of photoactive PS II complexes. An enhanced capability of nitroxide radicals to accept electrons from PS II correlates with their chemical structure. Nitroxide radicals NTI (2,2,5,5-tetramethyl-4-nitromethylene-3-imidazolidine-N-oxyl) and Tacet (4-hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl-acetate), containing polar groups, appear to be most efficient acceptors of electrons donated by PS II compared to neutral (TEMPOL, 4-hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl) or positively charged (Tamine, 4-amino-2,2,6,6-tetramethylpiperidine-l-oxyl) spin labels. We assume that enhanced reactivities of polar nitroxide radicals, NTI and Tacet, are determined (1) by their relatively high redox potentials, providing the possibility to accept electrons from PS II, and (2) by their affinities to the closest binding sites on the surface of PS II in the vicinity of the primary plastoquinone acceptor PQ_A (12-14 Å) or/and in the intraprotein cavity for the secondary plastoquinone PQ_B (~ 22 Å).

Mechanism of the formation of proton transfer pathways in photosynthetic reaction centers

The crystal structures of photosynthetic reaction centers from purple bacteria (PbRCs) and photosystem II show large structural similarity. However, the proposed mechanisms of proton transfer toward the terminal electron acceptor quinone (Q_B) are not consistent. In particular, not His-L190, which is an H-bond partner of Q_B, but rather Glu-L212, which is ∼6 Å away from Q_B, was assumed to be the direct proton donor for Q_B. We demonstrate that the H-bond between His-L190 and Q_B is a low-barrier H-bond, which facilitates proton transfer from singly protonated His-L190 to Q_B. Furthermore, Glu-L212 is not a direct H-bond donor for Q_B. However, it facilitates proton transfer toward deprotonated His-L190 via water molecules after Q_BH₂ forms and leaves the PbRC.

In photosynthetic reaction centers from purple bacteria (PbRCs) from Rhodobacter sphaeroides, the secondary quinone Q_B accepts two electrons and two protons via electron-coupled proton transfer (PT). Here, we identify PT pathways that proceed toward the Q_B binding site, using a quantum mechanical/molecular mechanical approach. As the first electron is transferred to Q_B, the formation of the Grotthuss-like pre-PT H-bond network is observed along Asp-L213, Ser-L223, and the distal Q_B carbonyl O site. As the second electron is transferred, the formation of a low-barrier H-bond is observed between His-L190 at Fe and the proximal Q_B carbonyl O site, which facilitates the second PT. As Q_BH₂ leaves PbRC, a chain of water molecules connects protonated Glu-L212 and deprotonated His-L190 forms, which serves as a pathway for the His-L190 reprotonation. The findings of the second pathway, which does not involve Glu-L212, and the third pathway, which proceeds from Glu-L212 to His-L190, provide a mechanism for PT commonly used among PbRCs.

ATR-FTIR Spectroelectrochemical Study on the Mechanism of the pH Dependence of the Redox Potential of the Non-Heme Iron in Photosystem II

The non-heme iron that bridges the two plastoquinone electron acceptors, Q_A and Q_B, in photosystem II (PSII) is known to have a redox potential (E_m) of ∼+400 mV with a pH dependence of ∼-60 mV/pH. However, titratable amino acid residues that are coupled to the redox reaction of the non-heme ion and responsible for its pH dependence remain unidentified. In this study, to clarify the mechanism of the pH dependent change of E_m(Fe²⁺/Fe³⁺), we investigated the protonation structures of amino acid residues correlated with the pH-induced E_m(Fe²⁺/Fe³⁺) changes using Fourier transform infrared (FTIR) spectroelectrochemistry combined with the attenuated total reflection (ATR) and light-induced difference techniques. Flash-induced Fe²⁺/Fe³⁺ ATR-FTIR difference spectra obtained at different electrode potentials in the pH range of 5.0-8.5 showed a linear pH dependence of E_m(Fe²⁺/Fe³⁺) with a slope of -52 mV/pH close to the theoretical value at 10 °C, the measurement temperature. The spectral features revealed that D1-H215, a ligand to the non-heme iron interacting with Q_B, was deprotonated to an imidazolate anion at higher pH with a pK_a of ∼5.6 in the Fe³⁺ state, while carboxylate groups from Glu/Asp residues present on the stromal side of PSII were protonated at lower pH with a pK_a of ∼5.7 in the Fe²⁺ state. It is thus concluded that the deprotonation/protonation reactions of D1-H215 and Glu/Asp residues located near the non-heme iron cause the pH-dependent changes in E_m(Fe²⁺/Fe³⁺) at higher and lower pH regions, respectively, realizing a linear pH dependence over a wide pH range.

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.

Tocopherol controls D1 amino acid oxidation by oxygen radicals in Photosystem II

Photosystem II (PSII) is an intrinsic membrane protein complex that functions as a light-driven water:plastoquinone oxidoreductase in oxygenic photosynthesis. Electron transport in PSII is associated with formation of reactive oxygen species (ROS) responsible for oxidative modifications of PSII proteins. In this study, oxidative modifications of the D1 and D2 proteins by the superoxide anion (O₂ ^•-) and the hydroxyl (HO^•) radicals were studied in WT and a tocopherol cyclase (vte1) mutant, which is deficient in the lipid-soluble antioxidant α-tocopherol. In the absence of this antioxidant, high-resolution tandem mass spectrometry was used to identify oxidation of D1:¹³⁰E to hydroxyglutamic acid by O₂ ^•- at the Pheo_D1 site. Additionally, D1:²⁴⁶Y was modified to either tyrosine hydroperoxide or dihydroxyphenylalanine by O₂ ^•- and HO^•, respectively, in the vicinity of the nonheme iron. We propose that α-tocopherol is localized near Pheo_D1 and the nonheme iron, with its chromanol head exposed to the lipid-water interface. This helps to prevent oxidative modification of the amino acid's hydrogen that is bonded to Pheo_D1 and the nonheme iron (via bicarbonate), and thus protects electron transport in PSII from ROS damage.

Capturing structural changes of the S1 to S2 transition of photosystem II using time-resolved serial femtosecond crystallography

Photosystem II (PSII) catalyzes light-induced water oxidation through an S i -state cycle, leading to the generation of di-oxygen, protons and electrons. Pump-probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture structural dynamics of light-sensitive proteins. In this approach, it is crucial to avoid light contamination in the samples when analyzing a particular reaction intermediate. Here, a method for determining a condition that avoids light contamination of the PSII microcrystals while minimizing sample consumption in TR-SFX is described. By swapping the pump and probe pulses with a very short delay between them, the structural changes that occur during the S1-to-S2 transition were examined and a boundary of the excitation region was accurately determined. With the sample flow rate and concomitant illumination conditions determined, the S2-state structure of PSII could be analyzed at room temperature, revealing the structural changes that occur during the S1-to-S2 transition at ambient temperature. Though the structure of the manganese cluster was similar to previous studies, the behaviors of the water molecules in the two channels (O1 and O4 channels) were found to be different. By comparing with the previous studies performed at low temperature or with a different delay time, the possible channels for water inlet and structural changes important for the water-splitting reaction were revealed.

Stable Tetrasubstituted Quinone Redox Reservoir for Enhancing Decoupled Hydrogen and Oxygen Evolution

Redox reservoirs (RRs) may be used to decouple the two half-reactions of water electrolysis, enabling spatial and temporal separation of hydrogen and oxygen evolution. Organic RRs are appealing candidates for this application; however, their instability limits their utility. Here, we show that a tetrathioether-substituted quinone, tetramercaptopropanesulfonate quinone (TMQ), exhibits significantly enhanced stability relative to anthraquinone-2,7-disulfonate (AQDS), the most effective organic RR reported previously. The enhanced stability, confirmed by symmetric flow battery experiments under relevant conditions, enables stable electrochemical production of H₂ and O₂ in a continuous flow electrolysis cell. The reduced RR, tetramercaptopropanesulfonate hydroquinone (TMHQ), is not susceptible to decomposition, while the oxidized state, TMQ, undergoes slow decomposition, evident only after sustained operation (>60 h). Analysis of the byproducts provides that basis for a decomposition mechanism, establishing a foundation for the design of new organic RRs with even better performance.

The Interaction between PsbT and the DE Loop of D1 in Photosystem II Stabilizes the Quinone-Iron Electron Acceptor Complex

The X-ray-derived Photosystem II (PS II) structure from the thermophilic cyanobacterium Thermosynechococcus vulcanus (Protein Data Bank entry 4UB6) indicates Phe239 of the DE loop of the D1 protein forms a hydrophobic interaction with Pro27 and Ile29 at the C-terminus of the 5 kDa PsbT protein found at the monomer-monomer interface of the PS II dimer. To investigate the importance of this interaction, we created the F239A and F239L mutants in Synechocystis sp. PCC 6803 through targeted mutagenesis of the D1:Phe239 residue into either an alanine or a leucine. Under moderate-light conditions, the F239A strain displayed reduced rates of oxygen evolution and impaired rates of fluorescence decay following a single-turnover actinic flash, while the F239L strain behaved like the control; however, under high-light conditions, the F239A and F239L strains grew more slowly than the control. Our results indicate the quinone-iron acceptor complex becomes more accessible to exogenously added electron acceptors in the F239A mutant and a ΔPsbT strain when compared with the control and F239L strains. This led to the hypothesis that the interaction between D1:Phe239 and the PsbT subunit is required to restrict movement of the DE loop of the D1 subunit, and we suggest disruption of this interaction may perturb the binding of bicarbonate to the non-heme iron and contribute to the signal for PS II to undergo repair following photodamage.

The Nature of the Short Oxygen-Oxygen Distance in the Mn4CaO6 Complex of Photosystem II Crystals

The O···O distance for a typical H-bond is ∼2.8 Å, whereas the radiation-damage-free structures of photosystem II (PSII), obtained using the X-ray free electron laser (XFEL), shows remarkably short O···O distances of ∼2 Å in the oxygen-evolving Mn₄CaO_5/6 complex. Herein, we report the protonation/oxidation states of the short O···O atoms in the XFEL structures using a quantum mechanical/molecular mechanical approach. The O5···O6 distance of 1.9 Å is reproduced only when O6 is an unprotonated O radical (O^•-) with Mn(IV)₃Mn(III), i.e., the S₃ state. The potential energy profile shows a barrier-less energy minimum region when O5···O6 = 1.90-2.05 Å (O^•- ↓) or 2.05-2.20 Å (O^•- ↑). Formation of such a short O5···O6 distance is not possible when O6 is OH^- with Mn(IV)₄. In the case in which the O5···O6 distance is 1.9 Å, it seems likely that the O radical species exists in the oxygen-evolving complex of the XFEL-S₃ crystals.

Proton-Coupled Electron Transfer for Photoinduced Generation of Two-Electron Reduced Species of Quinone

Purpose-built molecules that follow the fundamental process of photosynthesis have significance in developing better insight into the natural photosynthesis process. Quinones have a significant role as electron acceptors in natural photosynthesis, and their reduction is assisted through H-bond donation or protonation. The major challenge in such studies is to couple the multielectron and proton-transfer process and to achieve a reasonably stable charge-separated state for the elucidation of the mechanistic pathway. We have tried to address this issue through the design of a donor-acceptor-donor molecular triad (2RuAQ) derived from two equivalent [Ru(bpy)₃]²⁺ derivatives and a bridging anthraquinone moiety (AQ). Photoinduced proton-coupled electron transfer (PCET) for this molecular triad was systematically investigated in the absence and presence of hexafluoroisopropanol and p-toluenesulfonic acid (PTSA) using time-resolved absorption spectroscopy in the ultrafast time domain. Results reveal the generation of a relatively long-lived charge-separated state in this multi-electron transfer reaction, and we could confirm the generation of AQ^2- and Ru^III as the transient intermediates. We could rationalize the mechanistic pathway and the dynamics associated with photoinduced processes and the role of H-bonding in stabilizing charge-separated states. Transient absorption spectroscopic studies reveal that the rates of intramolecular electron transfer and the mechanistic pathways associated with the PCET process are significantly different in different solvent compositions having different polarities. In acetonitrile, a concerted PCET mechanism prevails, whereas the stepwise PCET reaction process is observed in the presence of PTSA. The results of the present study represent a unique model for the mechanistic diversity of PCET reactions.

Proton-Coupled Electron Transfers of Defense Phytochemicals in Sorghum (Sorghum bicolor (L.) Moench)

Sorghum (Sorghum bicolor (L.) Moench) produces a range of defense phytochemicals containing a quinone core structure: sorgoleone allelochemical, flavonoid phytoalexins, and a broad spectrum of polyphenols. Those phytochemicals react with the components of cellular and agroecosystems to form stable semiquinone radicals engaging in different proton-coupled electron transfer reactions. This unique redox reactivity of plant phenolics could be used to develop bioactive food ingredients and green pesticides. To achieve those application goals, chemical phenotyping methods sensitive to quinone-semiquinone-dihydroxybenzene redox cycles (e.g., electrochemical conversion with fluorescence detection) are in demand. Chemometrics-based fingerprinting tools could facilitate on-farm screening of target traits for breeding innovations.

Proton transfer pathway from the oxygen-evolving complex in photosystem II substantiated by extensive mutagenesis

We report a structure-based biological approach to identify the proton-transfer pathway in photosystem II. First, molecular dynamics (MD) simulations were conducted to analyze the H-bond network that may serve as a Grotthuss-like proton conduit. MD simulations show that D1-Asp61, the H-bond acceptor of H₂O at the Mn₄CaO₅ cluster (W1), forms an H-bond via one water molecule with D1-Glu65 but not with D2-Glu312. Then, D1-Asp61, D1-Glu65, D2-Glu312, and the adjacent residues, D1-Arg334, D2-Glu302, and D2-Glu323, were thoroughly mutated to the other 19 residues, i.e., 114 Chlamydomonas chloroplast mutant cells were generated. Mutation of D1-Asp61 was most crucial. Only the D61E and D61C cells grew photoautotrophically and exhibit O₂-evolving activity. Mutations of D2-Glu312 were less crucial to photosynthetic growth than mutations of D1-Glu65. Quantum mechanical/molecular mechanical calculations indicated that in the PSII crystal structure, the proton is predominantly localized at D1-Glu65 along the H-bond with D2-Glu312, i.e., pK_a(D1-Glu65) > pK_a(D2-Glu312). The potential-energy profile shows that the release of the proton from D1-Glu65 leads to the formation of the two short H-bonds between D1-Asp61 and D1-Glu65, which facilitates downhill proton transfer along the Grotthuss-like proton conduit in the S₂ to S₃ transition. It seems possible that D1-Glu65 is involved in the dominant pathway that proceeds from W1 via D1-Asp61 toward the thylakoid lumen, whereas D2-Glu312 and D1-Arg334 may be involved in alternative pathways in some mutants.

Reversible inhibition and reactivation of electron transfer in photosystem I

In photosystem I (PSI) complexes at room temperature electron transfer from A₁^- to F_X is an order of magnitude faster on the B-branch compared to the A-branch. One factor that might contribute to this branch asymmetry in time constants is TrpB673 (Thermosynechococcus elongatus numbering), which is located between A_1B and F_X. The corresponding residue on the A-branch, between A_1A and F_X, is GlyA693. Here, microsecond time-resolved step-scan FTIR difference spectroscopy at 77 K has been used to study isolated PSI complexes from wild type and TrpB673Phe mutant (WB673F mutant) cells from Synechocystis sp. PCC 6803. WB673F mutant cells require glucose for growth and are light sensitive. Photoaccumulated FTIR difference spectra indicate changes in amide I and II protein vibrations upon mutation of TrpB673 to Phe, indicating the protein environment near F_X is altered upon mutation. In the WB673F mutant PSI samples, but not in WT PSI samples, the phylloquinone molecule that occupies the A₁ binding site is likely doubly protonated following long periods of repetitive flash illumination at room temperature. PSI with (doubly) protonated quinone in the A₁ binding site are not functional in electron transfer. However, electron transfer functionality can be restored by incubating the light-treated mutant PSI samples in the presence of added phylloquinone.

Bicarbonate-Mediated CO2 Formation on Both Sides of Photosystem II

The effect of bicarbonate (HCO3-) on photosystem II (PSII) activity was discovered in the 1950s, but only recently have its molecular mechanisms begun to be clarified. Two chemical mechanisms have been proposed. One is for the electron-donor side, in which mobile HCO3- enhances and possibly regulates water oxidation by acting as proton acceptor, after which it dissociates into CO2 and H2O. The other is for the electron-acceptor side, in which (i) reduction of the QA quinone leads to the release of HCO3- from its binding site on the non-heme iron and (ii) the Em potential of the QA/QA•- couple increases when HCO3- dissociates. This suggested a protective/regulatory role of HCO3- as it is known that increasing the Em of QA decreases the extent of back-reaction-associated photodamage. Here we demonstrate, using plant thylakoids, that time-resolved membrane-inlet mass spectrometry together with 13C isotope labeling of HCO3- allows donor- and acceptor-side formation of CO2 by PSII to be demonstrated and distinguished, which opens the door for future studies of the importance of both mechanisms under in vivo conditions.

Stabilization of Photosystem II by the PsbT protein impacts photodamage, repair and biogenesis

Photosystem II (PS II) catalyzes the light-driven process of water splitting in oxygenic photosynthesis. Four core membrane-spanning proteins, including D1 that binds the majority of the redox-active co-factors, are surrounded by 13 low-molecular-weight (LMW) proteins. We previously observed that deletion of the LMW PsbT protein in the cyanobacterium Synechocystis sp. PCC 6803 slowed electron transfer between the primary and secondary plastoquinone electron acceptors Q_A and Q_B and increased the susceptibility of PS II to photodamage. Here we show that photodamaged ∆PsbT cells exhibit unimpaired rates of oxygen evolution if electron transport is supported by HCO₃^- even though the cells exhibit negligible variable fluorescence. We find that the protein environment in the vicinity of Q_A and Q_B is altered upon removal of PsbT resulting in inhibition of Q_A^- oxidation in the presence of 2,5-dimethyl-1,4-benzoquinone, an artificial PS II-specific electron acceptor. Thermoluminescence measurements revealed an increase in charge recombination between the S₂ oxidation state of the water-oxidizing complex and Q_A^- by the indirect radiative pathway in ∆PsbT cells and this is accompanied by increased ¹O₂ production. At the protein level, both D1 removal and replacement, as well as PS II biogenesis, were accelerated in the ∆PsbT strain. Our results demonstrate that PsbT plays a key role in optimizing the electron acceptor complex of the acceptor side of PS II and support the view that repair and biogenesis of PS II share an assembly pathway that incorporates both de novo synthesis and recycling of the assembly modules associated with the core membrane-spanning proteins.

The study of conformational changes in photosystem II during a charge separation

Photosystem II (PSII) is a multi-subunit pigment-protein complex and is one of several protein assemblies that function cooperatively in photosynthesis in plants and cyanobacteria. As more structural data on PSII become available, new questions arise concerning the nature of the charge separation in PSII reaction center (RC). The crystal structure of PSII RC from cyanobacteria Thermosynechococcus vulcanus was selected for the computational study of conformational changes in photosystem II associated to the charge separation process. The parameterization of cofactors and lipids for classical MD simulation with Amber force field was performed. The parametrized complex of PSII was embedded in the lipid membrane for MD simulation with Amber in Gromacs. The conformational behavior of protein and the cofactors directly involved in the charge separation were studied by MD simulations and QM/MM calculations. This study identified the most likely mechanism of the proton-coupled reduction of plastoquinone Q_B. After the charge separation and the first electron transfer to Q_B, the system undergoes conformational change allowing the first proton transfer to Q_B^- mediated via Ser264. After the second electron transfer to Q_BH, the system again adopts conformation allowing the second proton transfer to Q_BH^-. The reduced Q_BH₂ would then leave the binding pocket.

Redox potentials along the redox-active low-barrier H-bonds in electron transfer pathways

Local proton transfer along redox-active low-barrier H-bonds can alter the driving force or electronic coupling for electron transfer, as the redox potential values depend on the H⁺ position in low-barrier H-bonds.

Enhancement of electron accepting ability of para-benzoquinone by a single water molecule

Electron acceptors built upon the para-benzoquinone (pBQ) electrophore are ubiquitous in nature. Here, we present a frequency-resolved photoelectron spectroscopic study of the cold pBQ radical anion, pBQ-, solvated by a single water molecule, as commonly encountered in nature. Our results show that the electron accepting ability is enhanced by the single water molecule and by elevated temperatures.

SCC-DFTB-PIMD Method To Evaluate a Multidimensional Quantum Free-Energy Surface for a Proton-Transfer Reaction

The self-consistent charge density functional tight binding method was combined with the path-integral molecular dynamics method for the first time to evaluate the two-dimensional free-energy surface including nuclear quantum effects of a proton-transfer reaction in a 2,4-dichlorophenol-trimethylamine complex. A statistically converged two-dimensional quantum free-energy surface was evaluated by the multidimensional blue moon ensemble method. The accuracy was guaranteed by optimizing the repulsive potential between the sp³-hybridized nitrogen and hydrogen atoms in a SCC-DFTB3 parameter set for the system to reproduce high-level quantum chemical calculations. The present study illustrates the usefulness of this new approach to investigate nuclear quantum effects in various realistic proton-transfer reactions.