Water Network Dynamics Next to the Oxygen-Evolving Complex of Photosystem II

Reiss, Krystle; Morzan, Uriel N.; Grigas, Alex T.; Batista, Víctor S.

doi:10.3390/inorganics7030039

Cited by 16 publications

(27 citation statements)

References 42 publications

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“…Picosecond-long QM/MM dynamics provided new insights in the transition from the S2 to the S3 state (Bovi et al 2013) and from the S3 to the S4 state (Narzi et al 2018). The vibrational fingerprint of the oxygen-evolving complex was also studied using QM/ MM dynamics simulations as well as the water channels surrounding the oxygen-evolving cluster (Reiss et al 2019).…”

Section: Including Electronic Degrees Of Freedom Using Quantum Mechanmentioning

confidence: 99%

Molecular dynamics simulations in photosynthesis

Liguori¹,

Croce²,

Marrink

et al. 2020

Photosynth Res

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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.Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Section: Including Electronic Degrees Of Freedom Using Quantum Mechanmentioning

confidence: 99%

Molecular dynamics simulations in photosynthesis

Liguori¹,

Croce²,

Marrink

et al. 2020

Photosynth Res

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“…The distorted seat base of the chair is formed by three Mn, one Ca, and four oxygen atoms, and the back of the chair is formed by the last Mn atom, the so-called dangler Mn, which lifts out the oxygen from its central position in the cluster (Figure 3b) [50]. This suggests that Mn4 has a more flexible location than the other metal atoms [51], and it might function as a gate for releasing protons from the Mn 4 CaO 5 cluster [52,53]. In 2011, the oxo-bridges and exact distances among the individual metal atoms, along with the accurate orientation of the lateral amino acid binding residues, was revealed from the high-resolution structure of PSII at 1.9 Å produced by Umena et al [54].…”

Section: Manganese At the Active Site Of Water Oxidation In Photosmentioning

confidence: 99%

The Biochemical Properties of Manganese in Plants

Schmidt

Husted

2019

Plants

155

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Manganese (Mn) is an essential micronutrient with many functional roles in plant metabolism. Manganese acts as an activator and co-factor of hundreds of metalloenzymes in plants. Because of its ability to readily change oxidation state in biological systems, Mn plays and important role in a broad range of enzyme-catalyzed reactions, including redox reactions, phosphorylation, decarboxylation, and hydrolysis. Manganese(II) is the prevalent oxidation state of Mn in plants and exhibits fast ligand exchange kinetics, which means that Mn can often be substituted by other metal ions, such as Mg(II), which has similar ion characteristics and requirements to the ligand environment of the metal binding sites. Knowledge of the molecular mechanisms catalyzed by Mn and regulation of Mn insertion into the active site of Mn-dependent enzymes, in the presence of other metals, is gradually evolving. This review presents an overview of the chemistry and biochemistry of Mn in plants, including an updated list of known Mn-dependent enzymes, together with enzymes where Mn has been shown to exchange with other metal ions. Furthermore, the current knowledge of the structure and functional role of the three most well characterized Mn-containing metalloenzymes in plants; the oxygen evolving complex of photosystem II, Mn superoxide dismutase, and oxalate oxidase is summarized.

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“…RESP charges are used for the 5 μ-oxo ligands, four terminal waters of Ca 2+ and Mn4 as well as the primary OEC ligands D1-D170, E189, H332, E333, D342, A344, and CP43-E354. The ESP charges [37] are obtained using density functional theory at B3LYP/6-31G level using the Gaussian software package [57]. RESP charges were derived from the DFT-calculated ESP charges using the RESP program [58].…”

Section: Methodsmentioning

confidence: 99%

Proton egress pathway during the S₁–S₂transition of the Oxygen Evolving Complex of Photosystem II

Kaur

Zhang

et al. 2021

Preprint

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Photosystem II uses water as the ultimate electron source of the photosynthetic electron transfer chain. Water is oxidized to dioxygen at the Oxygen Evolving Complex (OEC), a Mn4CaO5 inorganic core embedded in the lumenal side of PSII. Water-filled channels are thought to bring in substrate water molecules to the OEC, remove the substrate protons to the lumen, and may transport the product oxygen. Three water-filled channels, denoted large, narrow, and broad, that extend from the OEC towards the aqueous surface more than 15 Å away are seen. However, the actual mechanisms of water supply to the OEC, the removal of protons to the lumen and diffusion of oxygen away from the OEC have yet to be established. Here, we combine Molecular Dynamics (MD), Multi Conformation Continuum Electrostatics (MCCE) and Network Analysis to compare and contrast the three potential proton transfer paths during the S1 to S2 transition of the OEC. Hydrogen bond network analysis shows that the three channels are highly interconnected with similar energetics for hydronium as calculated for all paths near the OEC. The channels diverge as they approach the lumen, with the water chain in the broad channel better interconnected that in the narrow and large channels, where disruptions in the network are observed at about 10 Å from the OEC. In addition, the barrier for hydronium translocation is lower in the broad channel, suggesting that a proton from the OEC could access the paths near the OEC, and likely exit to the lumen via the broad channel, passing through PsbO.

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Water Network Dynamics Next to the Oxygen-Evolving Complex of Photosystem II

Cited by 16 publications

References 42 publications

Molecular dynamics simulations in photosynthesis

Molecular dynamics simulations in photosynthesis

The Biochemical Properties of Manganese in Plants

Proton egress pathway during the S₁–S₂transition of the Oxygen Evolving Complex of Photosystem II

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Water Network Dynamics Next to the Oxygen-Evolving Complex of Photosystem II

Cited by 16 publications

References 42 publications

Molecular dynamics simulations in photosynthesis

Molecular dynamics simulations in photosynthesis

The Biochemical Properties of Manganese in Plants

Proton egress pathway during the S1–S2transition of the Oxygen Evolving Complex of Photosystem II

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Product

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Proton egress pathway during the S₁–S₂transition of the Oxygen Evolving Complex of Photosystem II