Characterizing the binding affinity and molecular interplay between quinoline yellow and pepsin

•Binding interaction of quinoline yellow with pepsin was investigated.•Experimental and modelling studies were applied to analyze the QY-Pepsin complex.•The conformation of pepsin was changed by QY.•QY affected the activity of pepsin.•Hydrophobic interactionsare the main forces involved in the interaction. Food dyes, including a broad spectrum of natural and synthetic dyes, are considered potentially hazardous materials that might pollute the environment and threaten human health. Hence, there is an urgent need to characterize the binding affinity and molecular interplay between these materials and biomolecules. Quinoline yellow (Qy) is a well-known synthetic food dye used in the food and pharmaceutical industries. However, its effect on the structure and function of enzymes is poorly understood. Here, we clarified the molecular interactions and binding affinity between Qy and pepsin using spectroscopic, molecular dynamics (MD), and computational approaches. Absorption spectral assays and fluorescence quenching analysis revealed that Qy could quench the intrinsic fluorescence of pepsin in the pepsin-Qy complex via a static quenching manner. Our data indicated Qy had a high binding constant and thereby affect the structure and function of pepsin. Thermodynamic parameters showed spontaneous binding of Qy on pepsin. The spectroscopic and molecular dynamic simulation analyses revealed that these binding interactions caused microenvironment alteration around the tryptophan chromophores and changes in the secondary and tertiary structures of pepsin. Furthermore, the MD simulations revealed that hydrogen bonds and Van der Waals interactions were the dominant forces in the formation of the pepsin-Qy complex. The circular dichroism (CD) spectroscopy analysis showed increased contents of α-Helix and Random Coil, as well as decreased content of β-sheet in the pepsin structure. Accordingly, MD simulations confirmed all the experimental results.