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Cow’s milk is considered an excellent protein source. However, the digestibility of milk proteins needs to be improved. This study aimed to evaluate the relationship between the functional properties of milk proteins and their structure upon microwave, ultrasound, and thermosonication treatments. The protein content, digestibility, and secondary-structure changes of milk proteins were determined. The results demonstrated that almost 35% of the proteins in the untreated samples had a α-helix structure and approximately 29% a β-sheet and turns structure. Regarding the untreated samples, the three treatments increased the α-helices and correspondingly decreased the β-sheets and turns. Moreover, the highest milk protein digestibility was observed for the ultrasound-treated samples (90.20–94.41%), followed by the microwave-treated samples (72.56–93.4%), whereas thermosonication resulted in a lower digestibility (68.76–78.81%). The milk protein content was reduced as the microwave processing time and the temperature increased. The final milk protein available in the sample was lower when microwave processing was conducted at 75 °C and 90 °C compared to 60 °C, whereas the ultrasound treatment significantly improved the protein content, and no particular trend was observed for the thermosonicated samples. Thus, ultrasound processing shows a potential application in improving the protein quality of cow’s milk.

Effects of Microwaves, Ultrasonication, and Thermosonication on the Secondary Structure and Digestibility of Bovine Milk Protein