This paper investigated the effects and underlying mechanisms of single-frequency (SFU: 50 kHz), dual-frequency (DFU: 35/50 kHz), and triple-frequency (TFU: 20/35/50 kHz) ultrasound treatments on lentil germination, nutritional properties, functional characteristics, and protein structural properties. The results demonstrated that, compared to the control (without sonication), DFU not only significantly improved lentil seed germination rate and germination index, reduced germination time by 16.7% (3 h), but also enhanced the nutritional properties of lentil flour. These changes included accelerating sugar degradation, promoting the accumulation of proteins, reducing sugars, and total phenolics, and significantly reducing phytic acid and tannin contents by stimulating related enzyme activities. In addition, DFU reduced viscosity and increased peak temperature, whereas TFU significantly improved the hydration characteristic index of germinated lentil flour for 120 h, which is key to enhancing the flour's processability in water-based food systems. Moreover, all ultrasound treatments increased free thiol content, and DFU significantly enhanced surface hydrophobicity, ionic bonds, hydrogen bonds, and hydrophobic interactions at 72 h. Besides, SFU and DFU significantly affected the fluorescence intensity by altering the spatial conformation of protein structures and the microenvironment around aromatic amino acids. SDS-PAGE analysis revealed that DFU and TFU induced the changes in protein molecular weight, degrading high-molecular-weight proteins into low-molecular-weight proteins. Collectively, these changes enhanced the nutritional value and processing quality of lentil flour. In conclusion, these findings indicated that DFU and TFU effectively improve the quality of germinated lentil flour, but differ in enhancement effects and can specifically satisfy the requirements of various processing scenarios.
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