Molecular Docking Research Between Nitrile/Phenol And Related Degrading Enzymes

Nitriles and phenols are the main components of industry wastewater.They are causing increasingly serious environmental pollution problems.This thesis uses the molecular docking method to study the binding mode and the interactions between these two kinds of toxic pollutants and related degrading enzymes during the biodegradation process. At the same time, the effect of Triton X-100on the removal of aqueous phenol catalyzed by laccase was studied to validate the docking theory.The continuing discharge of nitriles in various industrial processes has caused serious environmental consequences of nitrile pollution. Microorganisms possess several nitrile-degrading pathways by direct interactions of nitriles with nitrile-degrading enzymes. However, these interactions are largely unknown and difficult to experimentally determine but important for interpretation of nitrile metabolisms and design of nitrile-degrading enzymes with better nitrile-converting activity. Here, we undertook a molecular modeling study of enzyme-substrate binding modes in the bi enzyme pathway for degradation of nitrile to acid. Docking results showed that the top substrates having favorable interactions with nitrile hydratase from Rhodococcus erythropolis AJ270(ReNHase), nitrile hydratase from Pseudonocardia thermophila JCM3095(PtNHase) and amidase from Rhodococcus sp. N-771(RhAmidase) were benzonitrile,3-Cyanopyridine and L-Methioninamide, respectively. We further analyzed the interactional profiles of these top poses with corresponding enzymes, showing that specific residues within the enzyme’s binding pockets formed diverse contacts with substrates. This information on binding landscapes and interactional profiles is of great importance for the design of nitrile-degrading enzyme mutants with better oxidation activity toward nitriles or amides in the process of pollutant treatments.According to reports, the existence of surfactant can reduce the enzyme and oxidative polymerization product between the protective enzymes, which make it not inactivation. In addition, the interaction between the enzyme and the surface active agent can cause the conformation of the enzyme or active site changes, thus affecting the enzyme activity and stability.However, as far as we know, the action mechanism between the enzyme and the surface active agent is a lack of research. Molecular docking is a method which can predict the interactions between proteins and ligands.Effects of Triton X-100on the removal of aqueous phenol catalyzed by laccase were studied. The optimal concentration of Triton X-100was155μM to improve phenol removal when the concentrations of phenol and laccase were50mg/L and0.05mg/mL, respectively. Laccase activity was increased with Triton X-100at concentrations from31to930μM and the highest increasing was about17%by930μM Triton X-100. Triton X-100increased phenol removal efficiencies at phenol concentrations from50to600mg/L.. Molecular docking method was used to analyze the interactions of laccase with phenol or Triton X-100. Docking results showed that phenol formed hydrogen bonds and hydrophobic interactions with laccase, whereas Triton X-100formed hydrophobic interactions with laccase. The reaction of phenol removal was also characterized using UV spectra. The results indicated that Triton X-100had certain application potential for enhancing phenol removal catalyzed by laccase in water treatment or remediation.