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

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