Binding of Anionic Polyacrylamide with Amidase and Laccase under 298, 303, and 308 K: Docking and Molecular Dynamics Simulation Studies Combined with Experiments.

Abstract

Amidase and laccase play a key role in the degradation process of anionic polyacrylamide (HPAM). However, the largest challenge of HPAM enzymatic degradation is whether the enzyme can bind with a substrate for a period of time. Here, the most suitable complexes, namely, Rh Amidase-HPAM-2 and Bacillus subtilis (B. subtilis) laccase-HPAM-3, were obtained by docking, and they were carried out for molecular dynamics simulation (MDS) under 298, 303, and 308 K. MDS result analysis showed that Rh Amidase-HPAM-2 was the most stable at 298 K mainly due to a salt bridge and a hydrogen bond, and B. subtilis laccase-HPAM-3 was the most stable at 298 K mainly due to two electrostatic and hydrogen bonds. The LYS96 in Rh Amidase-HPAM-2 and LYS135 in B. subtilis laccase-HPAM-3 had been the most important in their binding process. The binding of Rh Amidase-HPAM-2 and B. subtilis laccase-HPAM-3 was optimal at 303 and 298 K, respectively. HPAM was degraded by mixed bacteria, and the optimal conditions were determined to be 308 K, initial pH = 7, and an inoculated dosage of 2 mL. Under these conditions, the degradation ratio reached 39.24%. The effect of parameters on the HPAM degradation ratio followed a decreasing order of temperature > initial pH > inoculated dosage. The HPAM codegradation mechanism was supposed by mixed bacteria according to test data. The mixed bacteria secreted both amidase and laccase, and they interacted jointly with HPAM. These results lay a theoretical foundation to design and modify the enzyme through mutation experiments in the future.