| Summary: | The purpose of this study is to obtain new antifreeze peptides (AFPs) that are natural, safe, and high activity from <i>Ctenopharyngodon idella</i> scales. The optimal hydrolysis conditions were investigated, and chromatography-based isolation was conducted using thermal hysteresis activity (THA) as an index. Molecular dynamic simulation (MDs) was explored to reveal the antifreeze mechanism of the AFPs. The results showed that the optimal hydrolysis conditions were 4000 U/g papain enzyme for 60 °C at pH 5.0 and substrate concentration (1:10) for 3 h, as unveiled by single-factor experiment results. The AFPs documented a THA of 2.7 °C when the T<sub>h</sub> was 1.3 °C. Hydrophilic peptide, named GCFSC-AFPs, with a THA of 5.09 °C when the T<sub>h</sub> was 1.1 °C was obtained after a series isolation of gel filtration, ion exchange, and reversed-phase HPLC chromatography. The AFPs had a molecular weight of 1107.54~1554.72 Da with three main peptides in the amino acid sequence of VGPAGPSGPSGPQ, RGSPGERGESGPAGPSG, and VGPAGPSGPSGPQG, respectively. The survival rate of yeast with GCFSC-AFPs reached 84.4% following one week of exposure at −20 °C. MDs indicated that GCFSC-AFPs interfered with the ice-water interaction and thus inhibited the ice crystallization process. Our data suggested that the GCFSC-AFPs were a novel and potential antifreeze agent in the food industry.
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