Role of Tryptophan W201 and W202 Residues of BaqA\(\bf \triangle\)C \(\bf \alpha\)-Amylase on Substrate Binding
Diandra Sekar Annisa, Ayra Ulpiyana, Fernita Puspasari, Reza Aditama, Dessy Natalia

Biochemistry Division, Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology.

Abstract

BaqA is an \(\alpha\)-Amylase from \(\it Bacillus\) \(\it aquimaris\) MKSC 6.2 that is isolated from a soft coral \(\it Sinularia\) \(\it sp\). which has the ability to degrade several raw starches, such as corn, rice, sago, cassava, and potato. Interestingly, BaqA has no starch binding domain (SBD) which is commonly found in raw starch degrading enzymes. Instead, \(\it in\) \(\it silico\) analysis suggested the presence of a surface binding site (SBS) consisting of double tryptophan (Trp201 and Trp202) in domain A and sugar-tongs residue (Tyr400) in domain C. The aim of this research was to study the potential role of tryptophan as SBS by employing molecular docking and molecular dynamics approaches. In this study, BaqA\(\triangle\)C which is a truncated BaqA lacking the C terminal 34 residues was used which has more solubility in water. Analysis was carried out to study the effect of the substitution of Trp201 and Trp202 into alanine (W201A, W202A, W201A/W202A) and phenylalanine (W201F) on affinity with substrates and protein stability. The BaqA\(\triangle\)C modeling was successfully carried out through the I-TASSER server with close to good results. It was found that mutations on BaqA\(\triangle\)C did not significantly affect protein stability. However, it leads to a decrease in the movement of residues at loop III located in domain B. Therefore, these results suggested that residues W201 and W202 might help to maintain the flexibility of loop III in domain B which is near the active center region of the protein. In addition, these studies reveal that the analog substrate could bind to the protein surface through interaction with the aromatic residue W201.

Keywords: BaqA\(\triangle\)C, surface binding site (SBS), double tryptophan, in silico mutation, molecular docking, molecular dynamics

Topic: Biokimia Komputasi