Modification of PAE-degrading Esterase(CarEW) for Higher Degradation Efficiency Through Integrated Homology Modeling, Molecular Docking, and Molecular Dynamics Simulation

Zhou, Mengying; Liu, Yu

doi:10.1007/s40242-022-1433-2

Cited by 4 publications

(2 citation statements)

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“…Molecular contacts between proteins and ligands in docking complexes play a crucial role in selecting effective ligands for target receptors . Molecular dynamics (MD) simulations are essential for studying protein conformational changes and ligand–protein binding mechanisms .…”

Section: Methodsmentioning

confidence: 99%

“…Molecular contacts between proteins and ligands in docking complexes play a crucial role in selecting effective ligands for target receptors. 27 Molecular dynamics (MD) simulations are essential for studying protein conformational changes and ligand−protein binding mechanisms. 28 It is performed using Desmond in Schrodinger software to analyze the kinetic process of the IBC−ENO1 complex obtained by the docking experiment.…”

Section: Molecular Dynamics Simulation Of the Ibc− Eno1 Complexmentioning

confidence: 99%

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Identification of Enolase 1 as a Potential Target for Magnaporthe oryzae: Integrated Proteomic and Molecular Dynamics Simulation

Gao

Zhang

et al. 2022

J. Chem. Inf. Model.

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Rice blast is an essential factor affecting rice yield and quality, which is caused by Magnaporthe oryzae (M. oryzae). Isobavachalcone (IBC) is a botanical fungicide derived from the seed extract of the Leguminosae plant Psoralea corylifolia L. and has shown an excellent rice blast control effect in field applications. To explore the potential targets of rice blast control, the analysis of the differentially expressed proteins (DEPs) between the liquid culture medium of mycelium treated by 10 mg/L of IBC for 2 h and the control group indicated that Enolase 1 (ENO1) was the most significantly down-regulated DEP with a fold change value of 0.305. In vitro experiments showed that after treating liquid culture mycelium with 10 mg/L of IBC for 0.5, 1, 2, 4, and 8 h, the enzymatic activity of ENO1 in the IBC experimental groups was 0.97, 0.75, 0.52, 0.44, and 0.39 times as much as in the control groups, respectively. To further explore the molecular interaction and binding mode between IBC and ENO1, the three-dimensional structure of ENO1 was established based on homology modeling. Molecular docking and molecular dynamics simulation showed that IBC had a pi−pi stacking effect with the residue TYR_365, a hydrogen bond interaction with the residue ARG_393, and hydrophobic interactions with non-polar residues ALA_361, LYS_362, and VAL_371 of ENO1. These findings indicated that ENO1 is a potential target of M. oryzae, which would pave the way for screening novel effective fungicides targeting ENO1.

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Section: Methodsmentioning

confidence: 99%

Section: Molecular Dynamics Simulation Of the Ibc− Eno1 Complexmentioning

confidence: 99%