Integrating Label-free proteomics and molecular dynamics to investigate the interactions between proteins and bioactive compounds in Rosa roxburghii tratt fermented by Lactobacillus acidophilus GIM1.208

Lactobacillus acidophilus GIM1.208 (LA) can improve flavor, enhance antioxidant and hypoglycemic activities of Rosa roxburghii Tratt (RRT). This study investigated the interactions between proteins and active compounds in RRT fermented by LA to reveal the underlying reasons for changes in flavor and activity. A total of 6239 proteins were characterized and quantified by Label-free proteomics, with their molecular weights were mainly concentrated in the range of 10–40 kDa. The 129 differential proteins screened were mainly enriched in compounds synthesis or transformation pathways, such as glycolysis. Integrated analysis of proteomics and metabolomics revealed a strong correlation between proteins and metabolites, especially β-glucosidase was closely correlation with flavonoids and triterpenoids. Additionally, molecular dynamics (MD) simulations have demonstrated that glycosides establish hydrogen bonds with the amino acids of β-glucosidase, while hydrophobic interactions serve as the primary driving force behind the binding process. Notably, Rosamutin exhibited the most significant binding energy with β-glucosidase (−66.257 kJ/mol). The results of the MD analysis further demonstrate the huge potential of LA β-glucosidase to transform glycosides in RRT. In summary, proteins in LA fermented RRT contribute to the consumption or synthesis of compounds, ultimately enhancing the flavor and activity of RRT. This study's results can provide a reference for the research of proteins and bioactive compounds of RRT.