How Does the QB Site Influence Propagate to the QA Site in Photosystem II?

Modulation of Electron Transfer Branches by Atrazine and Triazine Herbicides in Photosynthetic Reaction Centers

Quinone analogue molecules, functioning as herbicides, bind to the secondary quinone site, QB, in type-II photosynthetic reaction centers, including those from purple bacteria (PbRC). Here, we investigated the impact of herbicide binding on electron transfer branches, using herbicide-bound PbRC crystal structures and employing the linear Poisson-Boltzmann equation. In contrast to urea and phenolic herbicides [Fufezan, C. Biochemistry 2005, 44, 12780-12789], binding of atrazine and triazine did not cause significant changes in the redox-potential (Em) values of the primary quinone (QA) in these crystal structures. However, a slight Em difference at the bacteriopheophytin in the electron transfer inactive branch (HM) was observed between the S(-)- and R(+)-triazine-bound PbRC structures. This discrepancy is linked to variations in the protonation pattern of the tightly coupled Glu-L212 and Glu-H177 pairs, crucial components of the proton uptake pathway in native PbRC. These findings suggest the existence of a QB-mediated link between the electron transfer inactive HM and the proton uptake pathway in PbRCs.

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.

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.

Effects of Stromal and Lumenal Side Perturbations on the Redox Potential of the Primary Quinone Electron Acceptor QA in Photosystem II

The primary quinone electron acceptor Q_A is a key component in the electron transfer regulation in photosystem II (PSII), and hence accurate estimation of its redox potential, E_m(Q_A^-/Q_A), is crucial in understanding the regulatory mechanism. Although fluorescence detection has been extensively used for monitoring the redox state of Q_A, it was recently suggested that this method tends to provide a higher E_m(Q_A^-/Q_A) estimate depending on the sample status due to the effect of measuring light [Kato et al. (2019) Biochim. Biophys. Acta 1860, 148082]. In this study, we applied the Fourier transform infrared (FTIR) spectroelectrochemistry, which uses non-reactive infrared light to monitor the redox state of Q_A, to investigate the effects of stromal- and lumenal-side perturbations on E_m(Q_A^-/Q_A) in PSII. It was shown that replacement of bicarbonate bound to the non-heme iron with formate upshifted E_m(Q_A^-/Q_A) by ∼55 mV, consistent with the previous fluorescence measurement. In contrast, an E_m(Q_A^-/Q_A) difference between binding of 3-(3,4-dichlorophenyl)-1,1-dimethylurea and bromoxynil was found to be ∼30 mV, which is much smaller than the previous estimate, ∼100 mV, by the fluorescence method. This ∼30 mV difference was verified by the decay kinetics of the S₂Q_A^- recombination. On the lumenal side, Mn depletion hardly affected the E_m(Q_A^-/Q_A), confirming the previous FTIR result. However, removal of the extrinsic proteins by NaCl or CaCl₂ wash downshifted the E_m(Q_A^-/Q_A) by 14-20 mV. These results suggest that electron flow through Q_A is regulated by changes both on the stromal and lumenal sides of PSII.

Structural basis of light-harvesting in the photosystem II core complex

Photosystem II (PSII) is a membrane-spanning, multi-subunit pigment-protein complex responsible for the oxidation of water and the reduction of plastoquinone in oxygenic photosynthesis. In the present review, the recent explosive increase in available structural information about the PSII core complex based on X-ray crystallography and cryo-electron microscopy is described at a level of detail that is suitable for a future structure-based analysis of light-harvesting processes. This description includes a proposal for a consistent numbering scheme of protein-bound pigment cofactors across species. The structural survey is complemented by an overview of the state of affairs in structure-based modeling of excitation energy transfer in the PSII core complex with emphasis on electrostatic computations, optical properties of the reaction center, the assignment of long-wavelength chlorophylls, and energy trapping mechanisms.

Systematic High-Accuracy Prediction of Electron Affinities for Biological Quinones

Quinones play vital roles as electron carriers in fundamental biological processes; therefore, the ability to accurately predict their electron affinities is crucial for understanding their properties and function. The increasing availability of cost-effective implementations of correlated wave function methods for both closed-shell and open-shell systems offers an alternative to density functional theory approaches that have traditionally dominated the field despite their shortcomings. Here, we define a benchmark set of quinones with experimentally available electron affinities and evaluate a range of electronic structure methods, setting a target accuracy of 0.1 eV. Among wave function methods, we test various implementations of coupled cluster (CC) theory, including local pair natural orbital (LPNO) approaches to canonical and parameterized CCSD, the domain-based DLPNO approximation, and the equations-of-motion approach for electron affinities, EA-EOM-CCSD. In addition, several variants of canonical, spin-component-scaled, orbital-optimized, and explicitly correlated (F12) Møller-Plesset perturbation theory are benchmarked. Achieving systematically the target level of accuracy is challenging and a composite scheme that combines canonical CCSD(T) with large basis set LPNO-based extrapolation of correlation energy proves to be the most accurate approach. Methods that offer comparable performance are the parameterized LPNO-pCCSD, the DLPNO-CCSD(T₀ ), and the orbital optimized OO-SCS-MP2. Among DFT methods, viable practical alternatives are only the M06 and the double hybrids, but the latter should be employed with caution because of significant basis set sensitivity. A highly accurate yet cost-effective DLPNO-based coupled cluster approach is used to investigate the methoxy conformation effect on the electron affinities of ubiquinones found in photosynthetic bacterial reaction centers. © 2018 Wiley Periodicals, Inc.

Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex

Plastoquinone (PLQ) acts as an electron carrier between photosystem II (PSII) and the cytochrome b₆f complex. To understand how PLQ enters and leaves PSII, here we show results of coarse grained molecular dynamics simulations of PSII embedded in the thylakoid membrane, covering a total simulation time of more than 0.5 ms. The long time scale allows the observation of many spontaneous entries of PLQ into PSII, and the unbinding of plastoquinol (PLQol) from the complex. In addition to the two known channels, we observe a third channel for PLQ/PLQol diffusion between the thylakoid membrane and the PLQ binding sites. Our simulations point to a promiscuous diffusion mechanism in which all three channels function as entry and exit channels. The exchange cavity serves as a PLQ reservoir. Our simulations provide a direct view on the exchange of electron carriers, a key step of the photosynthesis machinery.

Modified molecular interactions of the pheophytin and plastoquinone electron acceptors in photosystem II of chlorophyll D-containing Acaryochloris marina as revealed by FTIR spectroscopy

Acaryochloris marina is a unique cyanobacterium that contains chlorophyll (Chl) d as a major pigment. Because Chl d has smaller excitation energy than Chl a used in ordinary photosynthetic organisms, the energetics of the photosystems of A. marina have been the subject of interest. It was previously shown that the redox potentials (E m's) of the redox-active pheophytin a (Pheo) and the primary plastoquinone electron acceptor (QA) in photosystem II (PSII) of A. marina are higher than those in Chl a-containing PSII, to compensate for the smaller excitation energy of Chl d (Allakhverdiev et al., Proc Natl Acad Sci USA 107: 3924-3929, 2010; ibid. 108: 8054-8058, 2011). To clarify the mechanisms of these E m increases, in this study, we have investigated the molecular interactions of Pheo and QA in PSII core complexes from A. marina using Fourier transform infrared (FTIR) spectroscopy. Light-induced FTIR difference spectra upon single reduction of Pheo and QA showed that spectral features in the regions of the keto and ester C=O stretches and the chlorin ring vibrations of Pheo and in the CO/CC stretching region of the Q A (-) semiquinone anion in A. marina are significantly different from those of the corresponding spectra in Chl a-containing cyanobacteria. These observations indicate that the molecular interactions, including the hydrogen bond interactions at the C=O groups, of these cofactors are modified in their binding sites of PSII proteins. From these results, along with the sequence information of the D1 and D2 proteins, it is suggested that A. marina tunes the E m's of Pheo and QA by altering nearby hydrogen bond networks to modify the structures of the binding pockets of these cofactors.

Structure/function/dynamics of photosystem II plastoquinone binding sites

Photosystem II (PSII) continuously attracts the attention of researchers aiming to unravel the riddle of its functioning and efficiency fundamental for all life on Earth. Besides, an increasing number of biotechnological applications have been envisaged exploiting and mimicking the unique properties of this macromolecular pigment-protein complex. The PSII organization and working principles have inspired the design of electrochemical water splitting schemes and charge separating triads in energy storage systems as well as biochips and sensors for environmental, agricultural and industrial screening of toxic compounds. An intriguing opportunity is the development of sensor devices, exploiting native or manipulated PSII complexes or ad hoc synthesized polypeptides mimicking the PSII reaction centre proteins as bio-sensing elements. This review offers a concise overview of the recent improvements in the understanding of structure and function of PSII donor side, with focus on the interactions of the plastoquinone cofactors with the surrounding environment and operational features. Furthermore, studies focused on photosynthetic proteins structure/function/dynamics and computational analyses aimed at rational design of high-quality bio-recognition elements in biosensor devices are discussed.

Some Photosystem II properties depending on the D1 protein variants in Thermosynechococcus elongatus

Cyanobacteria have multiple psbA genes encoding PsbA, the D1 reaction center protein of the Photosystem II complex which bears together with PsbD, the D2 protein, most of the cofactors involved in electron transfer reactions. The thermophilic cyanobacterium Thermosynechococcus elongatus has three psbA genes differently expressed depending on the environmental conditions. Among the 344 residues constituting each of the 3 possible PsbA variants there are 21 substitutions between PsbA1 and PsbA3, 31 between PsbA1 and PsbA2 and 27 between PsbA2 and PsbA3. In this review, we summarize the changes already identified in the properties of the redox cofactors depending on the D1 variant constituting Photosystem II in T. elongatus. This article is part of a special issue entitled: photosynthesis research for sustainability: keys to produce clean energy.

The nonheme iron in photosystem II

Photosystem II (PSII), the light-driven water:plastoquinone (PQ) oxidoreductase of oxygenic photosynthesis, contains a nonheme iron (NHI) at its electron acceptor side. The NHI is situated between the two PQs QA and QB that serve as one-electron transmitter and substrate of the reductase part of PSII, respectively. Among the ligands of the NHI is a (bi)carbonate originating from CO2, the substrate of the dark reactions of oxygenic photosynthesis. Based on recent advances in the crystallography of PSII, we review the structure of the NHI in PSII and discuss ideas concerning its function and the role of bicarbonate along with a comparison to the reaction center of purple bacteria and other enzymes containing a mononuclear NHI site.

Redirecting electron transfer in photosystem II from water to redox-active metal complexes

A negatively charged region on the surface of photosystem II (PSII) near Q(A) has been identified as a docking site for cationic exogenous electron acceptors. Oxygen evolution activity, which is inhibited in the presence of the herbicide 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), is recovered by adding Co(III) complexes. Thus, a new electron-transfer pathway is created with Co(III) as the new terminal electron acceptor from Q(A)(-). This binding site is saturated at ∼2.5 mM [Co(III)], which is consistent with the existence of low-affinity interactions with a solvent-exposed surface. This is the first example of a higher plant PSII in which the electron-transfer pathway has been redirected from the normal membrane-associated quinone electron acceptors to water-soluble electron acceptors. The proposed Co(III) binding site may enable efficient collection of electrons generated from photochemical water oxidation by PSII immobilized on an electrode surface.