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

Abstract

Apigenin is a vital flavonoid that has attracted considerable attention in recent years due to its potent health benefits. Pumpkin seed protein (PSP) is a valuable by-product after pumpkin seed processing. However, the non-covalent interaction mechanism between apigenin and PSP remains to be explored. Here, the structural and conformational changes and molecular mechanisms underlying their interaction were investigated using multi-spectroscopic analysis integrated with molecular simulation approaches. The experimental results indicated that apigenin statically quenched the intrinsic fluorescence of PSP, indicating that the interaction between them did occur. Thermodynamic analysis and computational simulation results showed that the driving forces between apigenin and PSP were the hydrophobic interactions that predominated. The binding of apigenin resulted in changes in the conformation, microenvironment, and surface hydrophobicity of PSP. Furthermore, it was revealed by molecular docking and molecular dynamic (MD) simulations that apigenin maintained binding stability in the hydrophobic pockets of the protein through its interaction with several key residues. Additionally, it was found that the movement strength and directions of individual resides were altered after apigenin binding, which is the molecular basis of protein structural and conformational changes induced by apigenin. This study may provide theoretical evidence for the potential application of PSP and apigenin complex products in the food industry.