Structural properties of the truncated and wild types of Taka-amylase: A molecular dynamics simulation and docking study

Abstract

In this work, structures of the native (Amyl-C) and truncated Taka amylase were compared by<br><br>molecular modeling methods. Using in silico enzyme engineering approach, 50 (Amyl-S1) and<br><br>100 (Amyl-S2) amino acids were eliminated from Amyl-C to produce the truncated forms.<br><br>Analysis of the tertiary structures showed that three essential domains of the enzyme including<br><br>super 8 , the barrel region, and the large cleft remained native in Amyl-<br><br>S1 and Amyl-S2. Secondary structures of Met112-Val118, Gly202-His211, Gln230-Asp233,<br><br>Phe292-Asp297 residues in Amyl-C, Amyl-S1, and Amyl-S2 remained unchanged. These<br><br>domains are necessary for catalytic function of alpha-amylase superfamily. Flexibility analysis of<br><br>the three forms was examined and it is obtained that by truncation, the flexibility of the Cterminal<br><br>domain was increased. This shows that C-terminal domain is essential for the stability<br><br>of the structure which is in agreement with experimental observations. However, Glu156, Gln<br><br>162, Gly234, Val 245, Asn260, Ser264, Asp 297 of Amyl-C had higher flexibility than those in<br><br>truncated enzymes. Maltoriose, Maltotetraose, Maltopentaose, Maltohexaose and maltoheptaose<br><br>as five substrates were docked to the three enzyme forms. Binding affinity of maltoheptaose was<br><br>higher in Amyl-C and Amyl-S1and lower in Amyl-S2 than that of Maltoriose. In all forms the<br><br>substrates were associated with three residues of the catalytic triad.