Revised force-field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9

Guerra, Federico; Adam, Suliman; Bondar, Ana‐Nicoleta

doi:10.1016/j.jmgm.2015.03.001

Cited by 19 publications

(15 citation statements)

References 33 publications

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“…Missing amino acids were added manually assuming four equal subunits followed by an energy minimization using the steepest decent algorithm (emtol = 100 kJ mol –1 nm –1 ). The parameters for Chla were obtained from refs − . After solvation and neutralization, adding 40 sodium ions, the system was energy-minimized using a steepest decent algorithm, followed by an NVT and an NPT equilibration of 100 ps each.…”

Section: Methodsmentioning

confidence: 99%

On the Stability of the Water-Soluble Chlorophyll-Binding Protein (WSCP) Studied by Molecular Dynamics Simulations

Lemke

Götze

2019

J. Phys. Chem. B

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The water-soluble chlorophyll-binding protein (WSCP) is assumed to be not a part of the photosynthetic process. Applying molecular dynamics (MD) simulations, we aimed to obtain insight into the exceptional stability of WSCP. We analyzed dynamical features such as the hydrogen bond network, flexibility, and force distributions. The WSCP structure contains two cysteines at the interfaces of every protein chain, which are in close contact with the cysteines of the other dimer. We tested if a connection of these cysteines between different protein chains influences the dynamical behavior to investigate any influences on the thermal stability. We find that the hydrogen bond network is very stable regardless of the presence or absence of the hypothetical disulfide bridges and/or the chlorophyll units. Furthermore, it is found that the phytyl chains of the chlorophyll units are extremely flexible, much more than what is seen in crystal structures. Nonetheless, they seem to protect a photochemically active site of the chlorophylls over the complete simulation time. Finally, we also find that a cavity in the chlorophyll-surrounding sheath exists, which may allow access for individual small molecules to the core of WSCP.

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Section: Methodsmentioning

confidence: 99%

On the Stability of the Water-Soluble Chlorophyll-Binding Protein (WSCP) Studied by Molecular Dynamics Simulations

Lemke

Götze

2019

J. Phys. Chem. B

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“…Currently, several all-atom and UA FFs are available and validated for all amino acids, several lipid classes, and different solvents (Oostenbrink et al 2004;Zhu et al 2012;Nerenberg and Head-Gordon 2018). Importantly for the photosynthetic community, nowadays several of these FFs have also been derived and validated for photosynthetic pigments and cofactors: most all-atom FFs (such as CHARMM and Amber) have been validated by comparing simulated properties against ab initio calculations (Damjanović et al 2002;Ceccarelli et al 2003;Karki and Roccatano 2011;Cerezo et al 2013;Guerra et al 2015;Adam et al 2018;Kim et al 2018). In the case of the Amber force field for Cars (Prandi et al 2016), this set of parameters has been specifically validated to reproduce selected spectral properties.…”

Section: Atomistic Force Fieldsmentioning

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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“…Pheophytin is involved in the process of electron transfer in PS II, working as a bridge of electrons between the chlorophyll P680 and plastoquinone 48 , 49 . Previous studies have investigated how this mechanism works and the function of pheophytin 50 , 51 . In this study, the increased levels of pheophytin may be due to induced chlorophyll degradation 52 , the stress, or a response that benefits the plant.…”

Section: Discussionmentioning

confidence: 99%

A metabolomic study of Gomphrena agrestis in Brazilian Cerrado suggests drought-adaptive strategies on metabolism

Melo

Abreu

Oliveira

et al. 2021

Sci Rep

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Drought is the main factor that limits the distribution and productivity of plant species. In the Brazilian Cerrado, the vegetation is adapted to a seasonal climate with long- and short-term periods of drought. To analyze the metabolic strategies under such conditions, a metabolomic approach was used to characterize Gomphrena agrestis Mart. (Amaranthaceae) a native species that grows under natural conditions, in a rock-field area. Roots and leaves material from native specimens were sampled along different seasons of the year and LC–MS and GC–MS analyzed for multiple chemical constituents. The datasets derived from the different measurements were combined and evaluated using multivariate analysis. Principal component analysis was used to obtain an overview of the samples and identify outliers. Later, the data was analyzed with orthogonal projection to latent structures discriminant analysis to obtain valid models that could explain the metabolite variations in the different seasons. Two hundred and eighty metabolites were annotated, generating a unique database to characterize metabolic strategies used to cope with the effects of drought. The accumulation of fructans in the thickened roots is consistent with the storage of carbons during the rainy season to support the energy demand during a long period of drought. The accumulation of Abscisic acid, sugars and sugar alcohols, phenolics, and pigment in the leaves suggests physiological adaptations. To cope with long-term drought, the data suggests that tissue water status and storage of reserves are important to support plant survival and regrowth. However, during short-term drought, osmoregulation and oxidative protection seems to be essential, probably to support the maintenance of active photosynthesis.

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Revised force-field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9

Cited by 19 publications

References 33 publications

On the Stability of the Water-Soluble Chlorophyll-Binding Protein (WSCP) Studied by Molecular Dynamics Simulations

On the Stability of the Water-Soluble Chlorophyll-Binding Protein (WSCP) Studied by Molecular Dynamics Simulations

Molecular dynamics simulations in photosynthesis

A metabolomic study of Gomphrena agrestis in Brazilian Cerrado suggests drought-adaptive strategies on metabolism

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