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• Low pH-shifting was used in black turtle bean protein isolate treatment. • Protein isolates were adjusted to neutral from pH 3.0, 2.0, 1.5, 1.0 incubations. • Protein was unfolded with exposure of buried hydrophobic residues after treatment. • Hydrophobic functionalities were improved, with decrease of hydrophilic properties. • Lower hemagglutination and immunoreactivity were obtained with better digestibility. Low pH-shifting was firstly applied in the black turtle bean (Phaseolus vulgaris L.) protein isolate treatment by acidic (pH 1.0–3.0) buffer incubation for 8 h, then was adjusted to pH 7.2 and kept 3 h for protein stabilizing. Mild loss of secondary structure was confirmed in the protein isolate after low pH-shifting treatment by CD and FT-IR analyses. Intrinsic fluorescence, UV spectra, surface hydrophobicity, SH content and SDS-PAGE analyses indicated the protein conformation was unfolded with the exposure of much more buried hydrophobic residues, which would result in the enhancement of emulsifying properties, foaming properties and fat holding capacity, and lead to the reduction of solubility and water holding capacity. Furthermore, lower immunoreactivity was observed by the ELISA, and improved digestibility was found in in vitro digestion assay. Our results suggested the low pH-shifting treatments would broaden the application of bean protein isolate with better hydrophobic processing functions and safety. [ABSTRACT FROM AUTHOR]