Molecular Dynamics Simulation of the Effect of Ascorbic Acid on the Protease Activity of Papain

In order to explore the effect of ascorbic acid on papain activity, the binding mechanism between them was investigated by molecular docking and molecular dynamics simulation. The findings demonstrated that ascorbic acid at all three concentrations tested (0.1, 0.2 and 0.3 mmol/L) could enhance papain activity with an average percentage of activation of 10%, 21%, and 28%, respectively, indicating that the higher the ascorbic acid concentration was, the more pronounced the activation effect was. The results of molecular dynamics simulation revealed that the root mean square deviation (RMSD) showed a slightly increasing trend after papain binding to ascorbic acid, and the average number of hydrogen bonds within the protease molecule decreased from 146 to 143. In addition, the total accessible surface area increased by 2.38 nm², the root mean square fluctuations of the active sites Asp158, His159 and Cys25 increased, and the gap between Cys25, which plays the primary catalytic role, and the two auxiliary amino acids decreased. Accordingly, we concluded that ascorbic acid can change the structure of papain’s active center, thereby activing the protease.