A comparative structural study on two immobilized metagenomic α-amylases by molecular docking

α-amylases are the major types of enzymes used in industries capable of catalyze starch hydrolysis. To facilitate reusability of the enzyme and address some problems associated with the free form such as lack of stability, the immobilization techniques are employed. Furthermore, to achieve more reliable results in modern research, we need structure-based modelling studies along with experimental studies. We immobilized two ↵-amylases named PersiAmy۲ and PersiAmy۳ identified from rumen metagenome on cellulose nanocrystals, reusability, and structural properties were investigated. Finally, the screening results based on the interactions between the ↵α-amylases and cellulose nanocrystals were studied using ۳۰۰ runs of molecular docking simulation, using Autodock ۴. Immobilized PersiAmy۲ and PersiAmy۳ provided higher thermal stability, and sustainability over issues of reusability compared to the free enzymes. Homology modeling, structural analysis, and molecular docking studies were also applied to simulate molecular interactions between enzymes and with one cellulose unit of Cellulose nanocrystals. Results were in agreement with the experimental findings and proved higher catalytic activity of immobilized PersiAmy۳ than PersiAmy۲. Based on computational results, hydrogen bond numbers were not su cient alone, to prove which binding pose is more favorable. So, H-bonds in both PersiAmy۲-ligand and PersiAmy۳-ligand complexes were equal, but value of binding free energy, number of residues in interactions with ligand in the binding site, and area of binding pose, had more favorable results in PersiAmy۳-ligand complex in comparison with PersiAmy۲-ligand complex

کلیدواژه ها:

amylase ، immobilization ، operational stability ، homology modeling ، structural analysis ، molecular docking simulation