Molecular dynamics simulation of interaction between high pressure carbon dioxide (HPCD) and phenylalanine ammonia-lyase (PAL)

High-pressure carbon dioxide (HPCD) could effectively suppress the yellowing phenomenon in Chinese water chestnut (CWC) by significantly inhibiting the activity of the key enzyme—phenylalanine ammonia-lyase (PAL). However, the molecular mechanism underlying this inhibition remains unclear. In this study, we investigated the structural changes and inhibition mechanisms of PAL from CWC subjected to HPCD treatment. Homology modeling was used to construct the 3D structure of CWC PAL. The results showed that CWC PAL was highly conserved and had higher α-helix content. Molecular dynamics simulations and molecular docking were utilized to investigate the non-covalent interaction between CO2 and PAL. Our findings revealed that CO2 induced conformational changes in PAL via hydrogen bonds, polar interactions, and hydrophobic interactions, thereby increasing PAL's α-helix structure and preventing the substrate L-Phe from entering its active site. Additionally, HPCD treatment caused the movement of the Phe-111 residue in the inner lid-loop, resulting in steric hindrance and destruction of the active center of PAL. These results provide a theoretical basis for expanding the application of HPCD in the food processing industry.