Molecular dynamic (in silico) modeling of structure–function of glutelin type-B 5-like from proso millet storage protein: effects of temperature and pressure

Akharume, Felix; Adedeji, Akinbode A.

doi:10.1007/s13197-022-05594-y

Cited by 3 publications

(1 citation statement)

References 29 publications

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“…Seed storage differs from other commodities in terms of simple transfers in and out, changes in quantity or variety, and involves scientific management of seed quality, storage conditions, and storage [1][2]. Seeds are susceptible to loss and damage from rodents during storage, leading to aging, deterioration and reduced germination [3]. According to statistics, the number of seeds lost due to improper storage in China is about 3% of the total storage volume every year, reaching tens of billions of kilograms, and this phenomenon is still worsening, with an economic loss of about 50 billion yuan [4][5].…”

Section: Introductionmentioning

confidence: 99%

Analysis of enzyme interference factors in millet storage based on machine learning

Chen,

Wei,

Wang

et al. 2023

Applied Mathematics and Nonlinear Sciences

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In this paper, we first investigate the peroxidase enzyme during millet storage, deeply analyze the characteristics of different types of grain bins during millet storage, and then summarize the peroxidase properties. Secondly, to extract the feature vector of the molecule, a descriptor was introduced, and on machine learning, SVM was used to construct a model of catalytic site MCD-MFEs and multiple catalytic sites SMAD-MFEs. Then, experimental materials were selected, experimental methods and measurement methods were determined, and an example analysis of machine learning-based enzymes during millet storage was performed, specifically from two aspects: model analysis and the study of peroxidase during millet storage. The results showed that the activity of millet peroxidase decreased by 92.2mg H2O2g−1, 90.4mg H2O2g−1, and 85.7mg H2O2g−1 for conventional, nitrogen-filled storage at 22°C. The activity of millet peroxidase decreased by 102.2mg H2O2g−, 98.8g H2O2g−, and 95.1mg H2O2g− The rate of reduction in peroxidase activity of millet stored in nitrogen-filled storage was not significantly different. This study was conducted to understand the enzyme change pattern during millet storage to provide a more intuitive and realistic reference for individual households to store grain.

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Section: Introductionmentioning

confidence: 99%

Analysis of enzyme interference factors in millet storage based on machine learning

Chen,

Wei,

Wang

et al. 2023

Applied Mathematics and Nonlinear Sciences

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Deciphering the interactions between altertoxins and glutenin based on molecular dynamic simulation: inspiration from detection

Yuan,

Chen,

Wen

et al. 2024

J Sci Food Agric

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BACKGROUNDMycotoxin contamination of food has been gaining increasing attention. Hidden mycotoxins that interact with biological macromolecules in food could make the detection of mycotoxins less accurate, potentially leading to the underestimation of the total exposure risk. Interactions of the mycotoxins alternariol (AOH) and alternariol monomethyl ether (AME) with high‐molecular glutenin were explored in this study.RESULTSThe recovery rates of AOH and AME (1, 2, and 10 μg kg−1) in three types of grains (rice, corn, and wheat) were relatively low. Molecular dynamics (MD) simulations indicated that AOH and AME bound to glutenin spontaneously. Hydrogen bonds and π‐π stacking were the primary interaction forces at the binding sites. Alternariol with one additional hydroxyl group exhibited stronger binding affinity to glutenin than AME when analyzing average local ionization energy. The average interaction energy between AOH and glutenin was −80.68 KJ mol−1, whereas that of AME was −67.11 KJ mol−1.CONCLUSIONThis study revealed the mechanisms of the interactions between AOH (or AME) and high‐molecular glutenin using MD and molecular docking. This could be useful in the development of effective methods to detect pollution levels. These results could also play an important role in the evaluation of the toxicological properties of bound altertoxins. © 2024 Society of Chemical Industry.

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In silico Analysis and Molecular Dynamic Modeling of Three-dimensional Structure of Glutelin type-B 5-like Proteins from Proso Millet: Effects of Temperature and Electric Field

Akharume

Singh

Korotkov

et al. 2023

Preprint

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This study determined the 3D structure of glutelin type-B 5-like (GTB) protein from proso millet using homology modeling and investigated the effects of simulated temperature and static electric field on its secondary structures, solvent accessibility surface area (SASA), the radius of gyration (Rg), root mean square deviation (RMSD), and total dipole moment. The result showed that the structure of GTB is majorly a protomer that comprises three monomers with one jelly-like β-barrel and two extended helix domains, and the remaining 35% as coils. Based on the molecular dynamic simulation, the secondary structure of the protein was not disrupted at temperatures between 300–400 K and static electric fields of between 0.1-3 V/nm, albeit the loss of a few amino acid residues. The RMSD increased significantly with an increase in temperature, static electric field, and simulation time. But the Rg and SASA decreased for the same conditions, suggesting that, the protein structure is compacting during thermal and electrical treatment.

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Molecular dynamic (in silico) modeling of structure–function of glutelin type-B 5-like from proso millet storage protein: effects of temperature and pressure

Cited by 3 publications

References 29 publications

Analysis of enzyme interference factors in millet storage based on machine learning

Analysis of enzyme interference factors in millet storage based on machine learning

Deciphering the interactions between altertoxins and glutenin based on molecular dynamic simulation: inspiration from detection

In silico Analysis and Molecular Dynamic Modeling of Three-dimensional Structure of Glutelin type-B 5-like Proteins from Proso Millet: Effects of Temperature and Electric Field

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