Computational studies of the O(2)-evolving complex of photosystem II and biomimetic oxomanganese complexes

The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules

Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and structural refinement of macrobiomolecules (e.g., proteins and nucleic acids). These methods are highly efficient, since they implement quantum chemistry techniques for modeling only the small part of the system (QM layer) that undergoes chemical modifications, charge transfer, etc., under the influence of the surrounding environment. The rest of the system (MM layer) is described in terms of molecular mechanics force fields, assuming that its influence on the QM layer can be roughly decomposed in terms of electrostatic interactions and steric hindrance. Common limitations of QM/MM methods include inaccuracies in the MM force fields, when polarization effects are not explicitly considered, and the approximate treatment of electrostatic interactions at the boundaries between QM and MM layers. This article reviews recent advances in the development of computational protocols that allow for rigorous modeling of electrostatic interactions in extended systems beyond the common limitations of QM/MM hybrid methods. We focus on the moving-domain QM/MM (MoD-QM/MM) methodology that partitions the system into many molecular domains and obtains the electrostatic and structural properties of the whole system from an iterative self-consistent treatment of the constituent molecular fragments. We illustrate the MoD-QM/MM method as applied to the description of photosystem II as well as in conjunction with the application of spectroscopically constrained QM/MM optimization methods, based on high-resolution spectroscopic data (extended X-ray absorption fine structure spectra, and exchange coupling constants).

A new quantum chemical approach to the magnetic properties of oligonuclear transition-metal complexes: application to a model for the tetranuclear manganese cluster of photosystem II

The reliable correlation of structural features and magnetic or spectroscopic properties of oligonuclear transition-metal complexes is a critical requirement both for research into innovative magnetic materials and for elucidating the structure and function of many metalloenzymes. We have developed a novel method that for the first time enables the extraction of hyperfine coupling constants (HFCs) from broken-symmetry density functional theory (BS-DFT) calculations on clusters. Using the geometry-optimized tetranuclear manganese complex [Mn(4)O(6)(bpy)(6)](4+/3+) as a model, we first examine in detail the calculation of exchange coupling constants J through the BS-DFT approach. Complications arising from the indeterminacy of experimentally fitted J constants are identified and analyzed. It is found that only the energy levels derived from Hamiltonian diagonalization are a physically meaningful basis for comparing theory and experiment. Subsequently, the proposed theoretical scheme is applied to the calculation of (55)Mn HFCs of the Mn(III,IV,IV,IV) state of the complex, which is similar to the S(2) state of the oxygen-evolving complex (OEC) in photosystem II of oxygenic photosynthesis. The new approach performs reliably and accurately, and yields calculated HFCs that can be directly compared with experimental data. Finally, we carefully examine the dependence of HFC on the J value and draw attention to the sensitivity of the calculated values to the exchange coupling parameters. The proposed strategy extends naturally to hetero-oligonuclear clusters of arbitrary shape and nuclearity, and hence is of general validity and usefulness in the study of magnetic metal clusters. The successful application of the new approach presented here is a first step in the effort to establish correlations between the available spectroscopic information and the structural features of complex metalloenzymes like OEC.

A possible evolutionary origin for the Mn4 cluster in photosystem II: from manganese superoxide dismutase to oxygen evolving complex

The recently published X-ray absorption fine structure of photosystem II provides a more detailed architecture of the oxygen-evolving complex (OEC) and the surrounding amino acids. In this paper, a comparison between manganese superoxide dismutase, dinuclear manganese catalase enzymes and the oxygen evolving complex in photosystem II is reported. The author suggests that the development of oxygenic photosynthesis occurred in steps, the first of which involved only one manganese ion (Mn(II)) that oxidized two water molecules to hydrogen peroxide and then oxygen.

Uncovering channels in photosystem II by computer modelling: current progress, future prospects, and lessons from analogous systems

Even prior to the publication of the crystal structures for photosystem II (PSII), it had already been suggested that water, O(2) and H(+) channels exist in PSII to achieve directed transport of these molecules, and to avoid undesirable side reactions. Computational efforts to uncover these channels and investigate their properties are still at early stages, and have so far only been based on the static PSII structure. The rationale behind the proposals for such channels and the computer modelling studies thus far are reviewed here. The need to take the dynamic protein into account is then highlighted with reference to the specific issues and techniques applicable to the simulation of each of the three channels. In particular, lessons are drawn from simulation studies on other protein systems containing similar channels.

A model of the oxygen-evolving center of photosystem II predicted by structural refinement based on EXAFS simulations

A refined computational structural model of the oxygen-evolving complex (OEC) of photosystem II (PSII) is introduced. The model shows that the cuboidal core Mn3CaO4 with a "dangler" Mn ligated to a corner mu4-oxide ion is maximally consistent with the positioning of the amino acids around the metal cluster as characterized by XRD models and high-resolution spectroscopic data, including polarized EXAFS of oriented single crystals and isotropic EXAFS. It is, therefore, natural to expect that the proposed structural model should be particularly useful to establish the structure of the OEC, consistently with high-resolution spectroscopic data, and for elucidating the mechanism of water-splitting in PSII as described by the intermediate oxidation states of the EC along the catalytic cycle.