Systematic exploration of the interactions between anionic polyacrylamide and manganese peroxidase based on docking and molecular dynamics simulations

Abstract

The biodegradation of anionic polyacrylamide (HPAM) mediated by manganese peroxidase (Mn P) has been experimentally discovered and reported by researchers, but the interaction mechanism of Mn P with HPAM at molecular level is still unclear. Here, the molecular mechanisms of HPAM structure models with Mn P obtained from Phanerochaete chrysosporium were investigated by docking and molecular dynamics (MD) simulations. The results indicate that both the number of H-bonds formed and key residues in MnP-HPAM-5 are the largest, leading to its maximal binding affinity. HPAM models contact with an active site of Mn P by H-bonds and hydrophobic interactions to maintain their stability. The binding of HPAM-5 results in the significant change and unfolding of enzyme structure, and the thicker hydration shell produced by a large amount of water molecule near the enzyme surface and the binding region makes HPAM-5 difficult to access the active site of enzyme. The enzyme structure is the most stable when it binds to HPAM-4, and the higher water molecules may form H-bonds with its binding region. These facilitate mass transfer, beneficial to its binding. This study provides the theoretical reference for designing the enzyme with higher activity and stability to enhance the degradation performance of HPAM.