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S1-state model of the O2-evolving complex of photosystem II.

ABSTRACT: We introduce a quantum mechanics/molecular mechanics model of the oxygen-evolving complex of photosystem II in the S(1) Mn(4)(IV,III,IV,III) state, where Ca(2+) is bridged to manganese centers by the carboxylate moieties of D170 and A344 on the basis of the new X-ray diffraction (XRD) model recently reported at 1.9 Å resolution. The model is also consistent with high-resolution spectroscopic data, including polarized extended X-ray absorption fine structure data of oriented single crystals. Our results provide refined intermetallic distances within the Mn cluster and suggest that the XRD model most likely corresponds to a mixture of oxidation states, including species more reduced than those observed in the catalytic cycle of water splitting.

SUBMITTER: Luber S

PROVIDER: S-EPMC3139771 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature

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S1-state model of the O2-evolving complex of photosystem II.

Luber Sandra S Rivalta Ivan I Umena Yasufumi Y Kawakami Keisuke K Shen Jian-Ren JR Kamiya Nobuo N Brudvig Gary W GW Batista Victor S VS

Biochemistry 20110627 29

We introduce a quantum mechanics/molecular mechanics model of the oxygen-evolving complex of photosystem II in the S(1) Mn(4)(IV,III,IV,III) state, where Ca(2+) is bridged to manganese centers by the carboxylate moieties of D170 and A344 on the basis of the new X-ray diffraction (XRD) model recently reported at 1.9 Å resolution. The model is also consistent with high-resolution spectroscopic data, including polarized extended X-ray absorption fine structure data of oriented single crystals. Our ...[more]

PMID: 21678908

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Computational insights into the O2-evolving complex of photosystem II.

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An e.x.a.f.s. study of the manganese O2-evolving complex in purified Photosystem II membrane fractions. The S1 and S2 states.

Project description:Manganese K-edge X-ray spectra have been obtained for Photosystem II samples isolated using Triton X-100 detergent and samples further purified by n-heptyl beta-D-thioglucoside detergent treatment to remove light-harvesting polypeptides and low-affinity calcium. The structure of the manganese complex is very similar for the two detergent preparations used. Analysis of the e.x.a.f.s. spectra for samples in the S1 and S2 states indicate changes in bond lengths for the shells of oxygen/nitrogen atoms. For the S1 state, oxygen shells at 0.181 and 0.193 nm (1.81 and 1.93 A) were observed and one manganese shell at 0.270 nm (2.70A). In the S2 state the oxygen bond lengths are longer at 0.184 and 0.200 nm (1.84 and 2.00 A). Additionally a shell of scatterers at 0.37 nm (3.7 A) was observed in both states which could be fitted to models with calcium scatterers at this distance.

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Project description:The laboratory synthesis of the oxygen-evolving complex (OEC) of photosystem II has been the objective of synthetic chemists since the early 1970s. However, the absence of structural information on the OEC has hampered these efforts. Crystallographic reports on photosystem II that have been appearing at ever-improving resolution over the past ten years have finally provided invaluable structural information on the OEC and show that it comprises a [Mn(3)CaO(4)] distorted cubane, to which is attached a fourth, external Mn atom, and the whole unit attached to polypeptides primarily by aspartate and glutamate carboxylate groups. Such a heterometallic Mn/Ca cubane with an additional metal attached to it has been unknown in the literature. This paper reports the laboratory synthesis of such an asymmetric cubane-containing compound with a bound external metal atom, [(1)]. All peripheral ligands are carboxylate or carboxylic acid groups. Variable-temperature magnetic susceptibility data have established 1 to possess an S = 9/2 ground state. EPR spectroscopy confirms this, and the Davies electron nuclear double resonance data reveal similar hyperfine couplings to those of other Mn(IV) species, including the OEC S(2) state. Comparison of the X-ray absorption data with those for the OEC reveal 1 to possess structural parameters that make it a close structural model of the asymmetric-cubane OEC unit. This geometric and electronic structural correspondence opens up a new front in the multidisciplinary study of the properties and function of this important biological unit.

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Structural changes in the oxygen-evolving complex of photosystem II induced by the S1 to S2 transition: A combined XRD and QM/MM study.

Project description:The S1 ? S2 transition of the oxygen-evolving complex (OEC) of photosystem II does not involve the transfer of a proton to the lumen and occurs at cryogenic temperatures. Therefore, it is commonly thought to involve only Mn oxidation without any significant change in the structure of the OEC. Here, we analyze structural changes upon the S1 ? S2 transition, as revealed by quantum mechanics/molecular mechanics methods and the isomorphous difference Fourier method applied to serial femtosecond X-ray diffraction data. We find that the main structural change in the OEC is in the position of the dangling Mn and its coordination environment.

| S-EPMC4230327 | biostudies-literature

Proton Translocation via Tautomerization of Asn298 During the S2-S3 State Transition in the Oxygen-Evolving Complex of Photosystem II.

Project description:In biological water oxidation, a redox-active tyrosine residue (D1-Tyr161 or YZ) mediates electron transfer between the Mn4CaO5 cluster of the oxygen-evolving complex and the charge-separation site of photosystem II (PSII), driving the cluster through progressively higher oxidation states S i ( i = 0-4). In contrast to lower S-states (S0, S1), in higher S-states (S2, S3) of the Mn4CaO5 cluster, YZ cannot be oxidized at cryogenic temperatures due to the accumulation of positive charge in the S1 → S2 transition. However, oxidation of YZ by illumination of S2 at 77-190 K followed by rapid freezing and charge recombination between YZ• and the plastoquinone radical QA•- allows trapping of an S2 variant, the so-called S2trapped state (S2t), that is capable of forming YZ• at cryogenic temperature. To identify the differences between the S2 and S2t states, we used the S2tYZ• intermediate as a probe for the S2t state and followed the S2tYZ•/QA•- recombination kinetics at 10 K using time-resolved electron paramagnetic resonance spectroscopy in H2O and D2O. The results show that while S2tYZ•/QA•- recombination can be described as pure electron transfer occurring in the Marcus inverted region, the S2t → S2 reversion depends on proton rearrangement and exhibits a strong kinetic isotope effect. This suggests that YZ oxidation in the S2t state is facilitated by favorable proton redistribution in the vicinity of YZ, most likely within the hydrogen-bonded YZ-His190-Asn298 triad. Computational models show that tautomerization of Asn298 to its imidic acid form enables proton translocation to an adjacent asparagine-rich cavity of water molecules that functions as a proton reservoir and can further participate in proton egress to the lumen.

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A Computational Study of the S2 State in the Oxygen-Evolving Complex of Photosystem II by Electron Paramagnetic Resonance Spectroscopy.

Project description:The S2 state produces two basic electron paramagnetic resonance signal types due to the manganese cluster in oxygen-evolving complex, which are influenced by the solvents, and cryoprotectant added to the photosystem II samples. It is presumed that a single manganese center oxidation occurs on S1 → S2 state transition. The S2 state has readily visible multiline and g4.1 electron paramagnetic resonance signals and hence it has been the most studied of all the Kok cycle intermediates due to the ease of experimental preparation and stability. The S2 state was studied using electron paramagnetic resonance spectroscopy at X-band frequencies. The aim of this study was to determine the spin states of the g4.1 signal. The multiline signal was observed to arise from a ground state spin ½ centre while the g4.1 signal generated at ≈140 K NIR illumination was proposed to arise from a spin 52 center with rhombic distortion. The 'ground' state g4.1 signal was generated solely or by conversion from the multiline. The data analysis methods used involved numerical simulations of the experimental spectra on relevant models of the oxygen-evolving complex cluster. A strong focus in this paper was on the 'ground' state g4.1 signal, whether it is a rhombic 52 spin state signal or an axial 32 spin state signal. The data supported an X-band CW-EPR-generated g4.1 signal as originating from a near rhombic spin 5/2 of the S2 state of the PSII manganese cluster.

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Project description:In recent years, there has been considerable interest in studies of catalytic metal clusters in metalloproteins based on Density Functional Theory (DFT) quantum mechanics/molecular mechanics (QM/MM) hybrid methods. These methods explicitly include the perturbational influence of the surrounding protein environment on the structural/functional properties of the catalytic centers. In conjunction with recent breakthroughs in X-ray crystallography and advances in spectroscopic and biophysical studies, computational chemists are trying to understand the structural and mechanistic properties of the oxygen-evolving complex (OEC) embedded in photosystem II (PSII). Recent studies include the development of DFT-QM/MM computational models of the Mn(4)Ca cluster, responsible for photosynthetic water oxidation, and comparative quantum mechanical studies of biomimetic oxomanganese complexes. A number of computational models, varying in oxidation and protonation states and ligation of the catalytic center by amino acid residues, water, hydroxide and chloride have been characterized along the PSII catalytic cycle of water splitting. The resulting QM/MM models are consistent with available mechanistic data, Fourier-transform infrared (FTIR) spectroscopy, X-ray diffraction data and extended X-ray absorption fine structure (EXAFS) measurements. Here, we review these computational efforts focused towards understanding the catalytic mechanism of water oxidation at the detailed molecular level.

| S-EPMC2350217 | biostudies-literature

Radiation Damage in XFEL: Case study from the oxygen-evolving complex of Photosystem II.

Project description:Structural changes induced by radiation damage in X-ray crystallography hinder the ability to understand the structure/function relationship in chemical reactions. Serial femtosecond crystallography overcomes this problem by exposing the sample to very short and intense laser pulse leading to measurement before destruction. Here we use molecular modeling to map the radiation damage during the 10-50?fs to the intensity, the energy and the time duration of the laser pulse on the oxygen-evolving complex (OEC) of photosystem II. In the model, the nuclei move classically in a fully quantum potential created by electron density under the effect of strong laser pulse in the Ehrenfest dynamics regime. The results show that the Mn-Mn and Mn-Ca distances are less affected by radiation damage due to the their heavy masses, while one ?-oxo bridge (O5) moves significantly. The radiation damage may induce conformational changes of the water ligands but only bond elongation for the amino acids ligands. These effects are relatively intensity independent from 10(16) to 10(17?)W/cm(2), but changes increase dramatically if the beam intensity is increased to 10(18) W/cm(2). In addition, the self amplified spontaneous emission (SASE) nature of the laser beam does not affect the dynamics of the ions.

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