Interaction of starches and amylases—An in silico study

In this study, protein sequence and structure alignment were performed to investigate the similarities between α-amylases (bacterial α-amylase, porcine pancreatic amylase, human pancreatic amylase, human salivary amylase). The α-amylases were further studied for the identification of active site residues. 3D structures of the starch polymorphs viz starch A and starch B were downloaded from the PolySac3Db database, and unit cell monomer was extracted from the downloaded structures. The crystallized ligands were used as a reference to model the binding poses of the starch A and starch B monomers into the active sites of the amylases. This was achieved by employing the “Pair Fitting” wizard, from PyMol. The binding mechanisms with the catalytic residues were then analyzed by viewing the polar interactions of the catalytic residues with the starch fragments. Multiple sequence alignment revealed a high degree of identity among the α-amylases of higher animals. However, the bacterial α-amylase did not show much sequence similarity with any of the α-amylases of higher animals. A good degree of structural similarity was observed among the human and porcine α-amylases. The common catalytic sites in most enzymes belonging to the α-amylase family dependent on Cl- are Asp197 and Asp300, which are known to act as nucleophiles, and Glu233, which acts as an acid/base catalyst. It was found that amylases showed different interactions with the glucose rings in both starch A and starch B. The present study is among the first to provide insights into the binding mechanisms of starch polymorphs viz., starch A and starch B, with α-amylases. The identification of the structural homology among the bacterial, porcine, and human α-amylases, and analysis of their catalytic binding mechanisms to the starch polymorphs allows us to bridge the knowledge gap in the in-vitro experiments performed using α-amylases from animal sources.