In vitro evaluation of the conjugations of neonicotinoids with transport protein: photochemistry, ligand docking and molecular dynamics studies

Abstract

The flexibility of ligand structures and the property of substituents in neonicotinoids play a pivotal role in protein–neonicotinoid and this type of biorecognition may have a great impact on the potential toxicity of these widely used agrochemicals.

Molecular Dynamics Simulation Prediction of the Partitioning Constants (KH, Kiw, Kia) of 82 Legacy and Emerging Organic Contaminants at the Water–Air Interface

“…To facilitate such studies, we provide a library of MD simulation input files for the compounds examined here []. We encourage efforts to expand this database; to refine it in the case of compounds identified as outliers, for example, using DFT simulations; , to use it to evaluate the affinity of OCs for other phases and interfaces; ,, to evaluate its performance against quantum mechanical approaches; to evaluate the importance of solvent effects in molecular docking simulations; ,,, and to apply machine learning approaches to identify clusters and trends within our compound library. , …”

“…All-atom molecular dynamics (MD) and density functional theory (DFT) simulations provide a potential alternative approach to filling the knowledge gap outlined above by enabling predictions of the partitioning behavior of environmental contaminants in explicitly simulated phases and multiphase systems. The promise of this approach is illustrated by its use in drug discovery and toxicology. − In the environmental sciences, increasing numbers of studies over the last two decades have used all-atom simulations to gain insight into the local coordination, energetics, and dynamics of OCs in natural systems. − However, few of these studies have generated information on the equilibrium constants controlling partitioning between phases or adsorption at interfaces. − …”

Construction of Fucoxanthin Vector Based on Binding of Whey Protein Isolate and Its Subsequent Complex Coacervation with Lysozyme

“…The variations of the RMSD regarding β-Lg, α-La, and BSA with or without FX were shown in Figure . Commonly, if the fluctuations of RMSD value for a typical dynamic system was kept within 0.1 nm, the system could be considered to reach a stable state of dynamic equilibrium . Obviously, the three non-covalent whey protein–FX complexes became stable from 12 ns.…”

“…Commonly, if the fluctuations of RMSD value for a typical dynamic system was kept within 0.1 nm, the system could be considered to reach a stable state of dynamic equilibrium. 42 Obviously, the three non-covalent whey protein−FX complexes became stable from 12 ns. Comparatively, the pure protein systems were equilibrated with some mild fluctuations over a time period of 20 ns.…”