First computational step towards the understanding of the antioxidant activity of the Phycocyanobilin:Ferredoxin Oxidoreductase in complex with biliverdin IXα

Cerón‐Carrasco, José P.; Jacquemin, Denis; Laurent, Adèle D.

doi:10.1016/j.comptc.2015.10.018

Cited by 3 publications

(4 citation statements)

References 25 publications

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“…As discussed later, the quantitative estimation of the redox potential is one of the important issues in the quantum chemistry. Some papers reported the good agreement of the computational results with the experimental ones [27,28], however, it is still a difficult task especially for large systems surrounded by the proteins. To avoid such difficulties, Noodleman and co-workers proposed a simplified method [7],…”

Section: Calculation Of the Vertical Ionization Potential Of The Reduced State (Ip(red))mentioning

confidence: 72%

“…In addition to the consideration of the surrounding protein, the quantitative estimation of the redox potential is also required for the further elucidation of the mechanism. There are many reports about the theoretical calculation of the redox potentials [15,16,27,28,30]. Those approaches must also be considered for the quantitative analyses and further discussions.…”

Section: Discussionmentioning

confidence: 99%

“…In experiments, a relative stability among several charge states is often discussed by using the redox potential (E redox ) that is defined by the difference in the free energies between the oxidized (ox) and reduced (red) states. In recent years, the redox potentials were calculated by the DFT calculations effectively [15,16,27,28]. As discussed later, the quantitative estimation of the redox potential is one of the important issues in the quantum chemistry.…”

Section: Calculation Of the Vertical Ionization Potential Of The Reduced State (Ip(red))mentioning

confidence: 99%

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Theoretical Study on Redox Potential Control of Iron-Sulfur Cluster by Hydrogen Bonds: A Possibility of Redox Potential Programming

et al. 2021

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The effect of hydrogen bonds around the active site of Anabaena [2Fe-2S] ferredoxin (Fd) on a vertical ionization potential of the reduced state (IP(red)) is examined based on the density functional theory (DFT) calculations. The results indicate that a single hydrogen bond increases the relative stability of the reduced state, and shifts IP(red) to a reductive side by 0.31–0.33 eV, regardless of the attached sulfur atoms. In addition, the IP(red) value can be changed by the number of hydrogen bonds around the active site. The results also suggest that the redox potential of [2Fe-2S] Fd is controlled by the number of hydrogen bonds because IP(red) is considered to be a major factor in the redox potential. Furthermore, there is a possibility that the redox potentials of artificial iron-sulfur clusters can be finely controlled by the number of the hydrogen bonds attached to the sulfur atoms of the cluster.

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Section: Calculation Of the Vertical Ionization Potential Of The Reduced State (Ip(red))mentioning

confidence: 72%

Section: Discussionmentioning

confidence: 99%

Section: Calculation Of the Vertical Ionization Potential Of The Reduced State (Ip(red))mentioning

confidence: 99%

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Theoretical Study on Redox Potential Control of Iron-Sulfur Cluster by Hydrogen Bonds: A Possibility of Redox Potential Programming

et al. 2021

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“…Cerón‐Carrasco, et al. reported QM and QM/QM’ calculations that explore the antioxidant activity of BV . Ikeda, et al.…”

Section: Methodsmentioning

confidence: 99%

QM/MM Investigation for Protonation States in a Bilin Reductase PcyA‐Biliverdin IXɑ Complex

et al. 2018

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Herein we report quantum mechanical/molecular mechanical (QM/MM) studies to investigate the most probable protonation states of active site amino acids and bound substrate based on a recently reported neutron diffraction structure of phycocyanobilin:ferredoxin oxidoreductase (PcyA) by Unno et al. This structure was considered to be bound in its initial state of biliverdin IXα (BV), which has the C-pyrrole ring in the deprotonated state. The protonation state of BV suggested by neutron and spectroscopic studies is a stable, two-electron reduced complex with a bound hydronium ion. Several ambiguities in the neutron structure were observed which prompted a further theoretical analysis of the structure. This structural investigation provides new understanding of the PcyA and BV protonation states not previously reported in the literature. Our calculations suggest that the hydronium ion (H O ) is energetically unfavorable, preferentially protonating the neighboring His88 residue and that the C-ring of BV is not protonated.

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Elucidation of Spartina dimethylsulfoniopropionate synthesis genes enables engineering of stress tolerant plants

Payet,

Bilham,

Kabir

et al. 2024

Nat Commun

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The organosulfur compound dimethylsulfoniopropionate (DMSP) has key roles in stress protection, global carbon and sulfur cycling, chemotaxis, and is a major source of climate-active gases. Saltmarshes are global hotspots for DMSP cycling due to Spartina cordgrasses that produce exceptionally high concentrations of DMSP. Here, in Spartina anglica, we identify the plant genes that underpin high-level DMSP synthesis: methionine S-methyltransferase (MMT), S-methylmethionine decarboxylase (SDC) and DMSP-amine oxidase (DOX). Homologs of these enzymes are common in plants, but differences in expression and catalytic efficiency explain why S. anglica accumulates such high DMSP concentrations and other plants only accumulate low concentrations. Furthermore, DMSP accumulation in S. anglica is consistent with DMSP having a role in oxidative and osmotic stress protection. Importantly, administration of DMSP by root uptake or over-expression of Spartina DMSP synthesis genes confers plant tolerance to salinity and drought offering a route for future bioengineering for sustainable crop production.

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First computational step towards the understanding of the antioxidant activity of the Phycocyanobilin:Ferredoxin Oxidoreductase in complex with biliverdin IXα

Cited by 3 publications

References 25 publications

Theoretical Study on Redox Potential Control of Iron-Sulfur Cluster by Hydrogen Bonds: A Possibility of Redox Potential Programming

Theoretical Study on Redox Potential Control of Iron-Sulfur Cluster by Hydrogen Bonds: A Possibility of Redox Potential Programming

QM/MM Investigation for Protonation States in a Bilin Reductase PcyA‐Biliverdin IXɑ Complex

Elucidation of Spartina dimethylsulfoniopropionate synthesis genes enables engineering of stress tolerant plants

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