Exploring the binding mechanism of pumpkin seed protein and apigenin: Spectroscopic analysis, molecular docking and molecular dynamics simulation

Pumpkin and Pumpkin Byproducts: Phytochemical Constitutes, Food Application and Health Benefits

“…The binding process between PSP and apigenin was primarily facilitated by hydrophobic interactions, which fostered modifications in the conformation, microenvironment, and surface hydrophobicity of the protein. Molecular docking analyses and molecular dynamic (MD) simulations illustrated the consistent binding of apigeninobic pockets . These findings suggested that the molecular interaction of pumpkin protein and polysaccharides with other bioactive components can be used to achieve functional proteins.…”

Application of Molecular Simulation Methods in Food Science: Status and Prospects

“…They identified van der Waals was the most favorable force to keep the binding, whereas polar solvation energy had negative effects. Liang et al 49 used GROMACS version 2019 with force field AMBER99SB-ILDN to explore the dynamics behaviors of pumpkin seed protein (PSP) and apigenin. They discovered that apigenin had a stable RMSD fluctuation (less than 4.0 Å, 200 ns) and that the binding free energy calculated by MM-PBSA was −59.39 kJ/mol, which indicated that apigenin was able to form a stable complex with PSP.…”

Molecular simulation for food protein–ligand interactions: A comprehensive review on principles, current applications, and emerging trends

“…This implicit model does not emphasize the specific structure and distribution of solvent molecules in the vicinity of the solute. It should be emphasized that the hydrophobic effect, which is frequently a dominant intermolecular force in the food protein–ligand interactions, can be embodied by nonpolar free energy terms in the solvent (Liang et al., 2023). The mathematical expressions of binding free energy are expressed as follows (Kumari et al., 2014; Xue et al., 2023): $$$$\begin{equation} \def\eqcellsep{&}\begin{array}{*{20}{c}} {{G}_{{\mathrm{solvent}}} = {G}_{{\mathrm{polar}}} + {G}_{{\mathrm{non - polar}}}} \end{array} \end{equation}$$$$ $$$$\begin{equation} \def\eqcellsep{&}\begin{array}{*{20}{c}} {{G}_{\mathrm{X}} = \left\langle {{E}_{{\mathrm{MM}}}} \right\rangle - TS + \left\langle {{G}_{{\mathrm{solvent}}}} \right\rangle } \end{array} \end{equation}$$$$ $$$$\begin{equation} \def\eqcellsep{&}\begin{array}{*{20}{c}} {\Delta {G}_{{\mathrm{binding}}} = {G}_{{\mathrm{complex}}} - {G}_{{\mathrm{food}}\,{\mathrm{protein}}} - {G}_{{\mathrm{ligand}}}} \end{array} \end{equation}$$$$where G solvent refers to the free energy required to transfer the solute from vacuum to solvent; G polar and G nonpolar refer to electrostatic and non‐electrostatic terms of solvation free energy, respectively; X refers to the compound, including food protein, ligand, or the complex of food protein and ligand; G X refers to the free energy of X.…”

“…In one study, variation in the number of H‐bonds between apigenin and pumpkin seed protein with time was shown, and apigenin acted as a donor and acceptor to form H‐bonds. MM‐PBSA was utilized to analyze various energy terms, including polar solvation energy, van der Waals energy, electrostatic energy, and SASA energy (Liang et al., 2023). These types of information are difficult to obtain through common physicochemical experiments.…”

“…This implicit model does not emphasize the specific structure and distribution of solvent molecules in the vicinity of the solute. It should be emphasized that the hydrophobic effect, which is frequently a dominant intermolecular force in the food protein-ligand interactions, can be embodied by nonpolar free energy terms in the solvent (Liang et al, 2023). The mathematical expressions of binding free energy are expressed as follows (Kumari et al, 2014;Xue et al, 2023):…”