Functional reconstitution of the primary quinone acceptor, QA, in the Photosystem II core complexes

Molecular dynamics simulations in photosynthesis

Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD.

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.

Vibrational spectroscopy to study the properties of redox-active tyrosines in photosystem II and other proteins

Tyrosine radicals play catalytic roles in essential metalloenzymes. Their properties--midpoint potential, stability...--or environment varies considerably from one enzyme to the other. To understand the origin of these properties, the redox tyrosines are studied by a number of spectroscopic techniques, including Fourier transform infrared (FTIR) and resonance Raman (RR) spectroscopy. An increasing number of vibrational data are reported for the (modified-) redox active tyrosines in ribonucleotide reductases, photosystem II, heme catalase and peroxidases, galactose and glyoxal oxidases, and cytochrome oxidase. The spectral markers for the tyrosinyl radicals have been recorded on models of (substituted) phenoxyl radicals, free or coordinated to metals. We review these vibrational data and present the correlations existing between the vibrational modes of the radicals and their properties and interactions formed with their environment: we present that the nu7a(C-O) mode of the radical, observed both by RR and FTIR spectroscopy at 1480-1515 cm(-1), is a sensitive marker of the hydrogen bonding status of (substituted)-phenoxyl and Tyr*, while the nu8a(C-C) mode may probe coordination of the Tyr* to a metal. For photosystem II, the information obtained by light-induced FTIR difference spectroscopy for the two redox tyrosines TyrD and TyrZ and their hydrogen bonding partners is discussed in comparison with those obtained by other spectroscopic methods.

Mobility of the primary electron-accepting plastoquinone QA of photosystem II in a Synechocystis sp. PCC 6803 strain carrying mutations in the D2 protein

Upon introduction of random mutations in a region of the psbDI gene that encodes the D2 protein in the cyanobacterium Synechocystis sp. PCC 6803, an obligate photoheterotrophic mutant was isolated that contained three mutations: V247M, A249T, and M329I. This mutant evolved oxygen in the absence of added electron acceptors, but oxygen evolution was inhibited by micromolar concentrations of several artificial quinones. Complementation analysis showed that the V247M and/or A249T mutations were responsible for this phenotype. Using fluorescence induction and decay measurements, the site of inhibition by the quinones was found to be at the level of the primary electron-accepting quinone in photosystem II, QA. Duroquinone inhibited by blocking reduction of QA, and in the presence of other quinones such as 2,5-dichloro-p-benzoquinone, 2, 5-dimethyl-p-benzoquinone, and p-benzoquinone, QA could be reduced but could not efficiently transfer an electron to QB. To distinguish the effects of the V247M and A249T mutations, single mutants were created. V247M was photoautotrophic and had an essentially normal phenotype. The A249T mutant, although photoautotrophic, was affected by artificial quinones, but less than the mutant carrying both the V247M and A249T changes. The results indicate a decreased plastoquinone affinity at the QA site in the strains carrying a A249T mutation, such that after dark-adaptation a significant percentage of the QA sites is empty or is occupied by an artificial quinone. In light, the percentage of photosystem II centers with plastoquinone bound at the QA site appears to increase, which may be due in part to an increased affinity of the semiquinone versus that of the quinone at the QA site.

Hydrogen bonding of redox-active tyrosine Z of photosystem II probed by FTIR difference spectroscopy

The TyrZ./TyrZ FTIR difference spectrum is reported for the first time in Mn-depleted photosystem II (PS II)-enriched membranes of spinach, in PS II core complexes of Synechocystis sp. PCC 6803 WT, and in the mutant lacking TyrD (D2-Tyr160Phe). In Synechocystis, the v7'a(CO) and delta(COH) infrared modes of TyrZ are proposed to account at 1279 and 1255 cm-1. The frequency of these modes indicate that TyrZ is protonated at pH 6 and involved in a strong hydrogen bond to the side chain of a histidine, probably D1-His190. A positive signal at 1512 cm-1 is assigned to the v(CO) mode of TyrZ. on the basis of the 27 cm-1 downshift observed upon 13C-Tyr labeling at the Tyr ring C4 carbon. A second IR signal, at 1532 cm-1, is tentatively assigned to the v8a(CC) mode of TyrZ.. The frequency of the v(CO) mode of TyrZ. at 1512 cm-1 is comparable to that observed at 1513 cm-1 for the Tyr. obtained by UV photochemistry of tyrosinate in solution, while it is higher than that of TyrD. in WT PS II at 1503 cm-1 and that of non-hydrogen-bonded TyrD. in the D2-His189Gln mutant at 1497 cm-1 [Hienerwadel, R., Boussac, A., Breton, J., Diner, B. A., and Berthomieu, C. (1997) Biochemistry 36, 14712-14723]. This latter work and the present FTIR study suggest that hydrogen bonding induces an upshift of the v(CO) IR mode of tyrosyl radicals and that TyrZ. forms (a) stronger hydrogen bond(s) than TyrD. in WT PS II. Alternatively, the frequency difference between TyrZ. and TyrD. v(CO) modes could be explained by a more localized positive charge near the tyrosyl radical oxygen of TyrD. than TyrZ.. The TyrZ./TyrZ spectrum obtained in Mn-depleted PS II membranes of spinach shows large similarities with the S3'/S2' spectrum characteristic of radical formation in Mn-containing but Ca(2+)-depleted PS II, in support of the assignment using ESEEM of TyrZ. as being responsible for the split EPR signal observed upon illumination in these conditions [Tang, X.-S., Randall, D. W., Force, D. A., Diner, B. A., and Britt, R. D. (1996) J. Am. Chem. Soc. 118, 7638-7639]. The peak at 1514 cm-1 is assigned to the v(CO) mode of TyrZ. in these preparations, which indicates that Mn depletion only very slightly perturbs the immediate environment of TyrZ. phenoxyl.

Effect of 13C-, 18O- and 2H-labeling on the infrared modes of UV-induced phenoxyl radicals

The structure and environment of redox active tyrosines present in several metalloenzymes can be studied by resonance Raman spectroscopy or Fourier transform infrared difference spectroscopy. Assignments of the vibrational modes in vivo often requires in vitro studies on model compounds. This approach is briefly reviewed. New results are shown on the influence of isotope-labeling on the infrared spectra of tyrosine, [Formula: see text] and phenol radicals obtained in vitro by UV-irradiation. The infrared spectra of the radicals are dominated by the [Formula: see text] mode at 1515-1504 cm(-1). The frequency shifts induced on this mode by (13)C- (2)H-, and (18)O-labeling are reported.

Electron paramagnetic resonance and mutational analyses revealed the involvement of photosystem II-L subunit in the oxidation step of Tyr-Z by P680+ to form the Tyr-Z+P680Pheo- state in photosystem II

To reveal the molecular mechanism of involvement of photosystem II (PSII)-L protein in the electron transfer in PSII, effects of mutations in PSII-L on the photochemistry of PSII were investigated by means of electron paramagnetic resonance (EPR) and flash photolysis. Wild type and a series of mutant versions of PSII-L were overproduced in Escherichia coliand chromatographically purified. Plastoquinone 9 (PQ-9) depleted PSII reaction center core complex consisting of CP47/D1/D2/Cytb-559/PSII-I/PSII-W was prepared and reconstituted with the wild type and each mutant version of PSII-L together with or without PQ-9. EPR signal indicating the formation of Tyr-Z+P680Pheo- state upon room-temperature illumination disappeared in CP47/D1/D2/Cytb-559/PSII-I/PSII-W, and it was recovered when the complex was reconstituted with the wild-type PSII-L. Mutation of a few amino acid residues in the carboxyl-terminal region of PSII-L, such as substitution of a triad of Tyr34, Phe35, and Phe36 by Leu, selectively resulted in the loss of the capability of PSII-L to recover the light-induced formation of Tyr-Z+P680Pheo- state in the reconstituted complex. Hydropathy profile of PSII-L suggests that it spans the membrane once by a hydrophobic stretch of the carboxyl-terminal side as its carboxyl end to face to the lumen. If this is the case, the amino acid residues essential for PSII-L to function are expected to be located close to the donor side of P680, suggesting the interaction of PSII-L with Tyr-Z (and/or Tyr-D) or P680 to facilitate the oxidation of Tyr-Z by P680+ to form Tyr-Z+P680Pheo- state in PSII. Evidence against PSII-L being involved in the electron transfer from Pheo- to QA was obtained by the flash photolysis experiments.

A difference Fourier transform infrared spectroscopic study of chlorophyll oxidation in hydroxylamine-treated photosystem II

In oxygenic photosynthesis, photosystem II is the chlorophyll-containing reaction center that carries out the light-induced transfer of electrons from water to plastoquinone. Fourier transform infrared spectroscopy can be used to obtain information about the structural changes that accompany electron transfer in photosystem II. The vibrational difference spectrum associated with the reduction of photosystem II acceptor quinones is of interest. Previously, a high concentration of the photosystem II donor, hydroxylamine, has been used to obtain a spectrum attributed to QA- -QA (Berthomieu, C., Nabedryk, E., Mantele, W. and Breton, J. FEBS Lett. (1990) 269, 363). Here, we use electron paramagnetic resonance, Fourier transform infrared spectroscopy, and 15N isotopic labeling to show that the difference infrared spectrum, obtained under these conditions, also exhibits a contribution from the oxidation of chlorophyll.

L protein, encoded by psbL, restores normal functioning of the primary quinone acceptor, QA, in isolated D1/D2/CP47/Cytb-559/I photosystem II reaction center core complex

Plastoquinone-9 (PQ-9)-depleted PSII reaction center core complex, consisting of CP47/D1/D2/Cytb-559/I, was isolated from spinach PSII particles. PQ-9, lipids and several proteins were extracted from the original PSII particles and separated by several steps of chromatography to be reconstituted into the isolated complex. PQ-9 reconstituted in the complex with the help of thylakoid lipids (digalactosyldiglyceride) did not function as QA by itself. However, PQ-9 simultaneously reconstituted with L protein and the thylakoid lipids successfully functioned as QA in the complex. Other proteins of PSII origin, such as CP43, H, K, nuclear encoded 4.1 and 5.0 kDa proteins, are unable to restore the QA activity in the complex.

Functional characterization of mutant strains of the cyanobacterium Synechocystis sp. PCC 6803 lacking short domains within the large, lumen-exposed loop of the chlorophyll protein CP47 in photosystem II

Several autotrophic mutant strains of Synechocystis sp. PCC 6803 carrying short deletions or a single-site mutation within the large, lumen-exposed loop (loop E) of the chlorophyll a-binding photosystem II core protein, CP47, are analyzed for their functional properties by measuring the flash-induced pattern of thermoluminescence, oxygen yield, and fluorescence quantum yield. A physiological and biochemical characterization of these mutant strains has been given in two previous reports [Eaton-Rye, J.J., & Vermaas, W.F.J. (1991) Plant Mol. Biol. 17, 1165-1177; Haag, E., Eaton-Rye, J.J., Renger, G., & Vermaas, S. F.J. (1993) Biochemistry 32, 4444-4454]. The results of the present study show that deletion of charged and conserved amino acids in a region roughly located between residues 370 and 390 decreases the binding affinity of the extrinsic PS II-O protein to photosystem II. Marked differences with PSII-O deletion mutants are observed with respect to Ca2+ requirement and the flash-induced pattern of oxygen evolution. Under conditions where a sufficient light activation is provided, the psbB mutants assayed in this study reveal normal S-state parameters and lifetimes. The results bear two basic implications: (i) the manganese involved in water oxidation can still be bound in a functionally normal or only slightly distorted manner, and (ii) the binding of the extrinsic PS II-O protein to photosystem II is impaired in mutants carrying a deletion in the domain between residues 370 and 390, but the presence of the PS II-O protein is still of functional relevance for the PS II complex, e.g., for maintenance of a high-affinity binding site for Ca2+ and/or involvement during the process of photoactivation.