(1) Background: Protein–polyphenol interactions have been widely studied regarding their influence on the properties of both protein and the ligands. As an important protein material in the food industry, soybean protein isolate (SPI) experiences interesting changes through polyphenols binding. (2) Methods: In this study, a molecular docking and virtual screening method was established to evaluate the SPI–polyphenol interaction. A compound library composed of 33 commonly found food source polyphenols was used in virtual screening. The binding capacity of top-ranking polyphenols (rutin, procyanidin, cyanidin chloride, quercetin) was validated and compared by fluorescence assays. (3) Results: Four out of five top-ranking polyphenols in virtual screening were flavonoids, while phenolic acids exhibit low binding capacity. Hydrogen bonding and hydrophobic interactions were found to be dominant interactions involved in soybean protein–polyphenol binding. Cyanidin chloride exhibited the highest apparent binding constant (Ka), which was followed by quercetin, procyanidin, and rutin. Unlike others, procyanidin addition perturbed a red shift of SPI fluorescence, indicating a slight conformational change of SPI. (4) Conclusions: These results suggest that the pattern of SPI–polyphenol interaction is highly dependent on the detailed structure of polyphenols, which have important implications in uncovering the binding mechanism of SPI–polyphenol interaction.
Soybean protein isolate (SPI) and small molecule interactions have drawn more and more attention regarding their benefits for both parts, while research on large-scale investigations and comparisons of different compounds is absent. In this study, a high throughput virtual screening was applied on a phytochemical database with 1130 compounds to pinpoint the potential SPI binder. Pentagalloylglucose, narcissoside, poliumoside, isoginkgetin, and avicurin were selected as the top-five ranking molecules for further validation. Fluorescence quenching assays illustrated that isoginkgetin has a significantly higher apparent binding constant (Ka) of (0.060 ± 0.020) × 106 L·mol−1, followed by avicularin ((0.058 ± 0.010) × 106 L·mol−1), pentagalloylglucose ((0.049 ± 0.010) × 106 L·mol−1), narcissoside ((0.0013 ± 0.0004) × 106 L·mol−1), and poliumoside ((0.0012 ± 0.0006) × 106 L·mol−1). Interface characterization by MD simulation showed that protein residues E172, H173, G202, and V204 are highly involved in hydrogen bonding with the two carbonyl oxygens of isoginketin, which could be the crucial events in SPI binding. Van der Waals force was identified as the major driven force for isoginketin binding. Our study explored SPI–phytochemical interaction through multiple strategies, revealing the molecular binding details of isoginkgetin as a novel SPI binder, which has important implications for the utilization of the SPI–phytochemical complex in food applications.
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