The interaction of pepsin with sunset yellow food additive (SY) was studied by fluorescence spectroscopy and molecular dynamics simulation. The experimental results indicated that SY can quench the fluorescence of pepsin with static quenching. The apparent binding constant Ka and binding site number n were evaluated at different temperatures. Thermodynamic analysis suggests that SY interact with pepsin spontaneously by van der Waal’s forces and hydrogen bond formation. Three‐dimensional fluorescence spectra showed that pepsin undergoes a slightly conformation change when it interacts with SY. The molecular dynamics simulation (MD) revealed that the binding site is located mainly on the tyrosine residues at the entrance of the active site of pepsin and the main interactions occurred between SY and pepsin are hydrogen bond and stacking interactions, according to experimental results. Furthermore, the binding between SY and pepsin can inhibit pepsin activity. Our MD results showed that the SY prevents substrate from entering the active site by making a barrier at the entrance of the active site, reducing the pepsin activity
