Accelerated molecular dynamics study to compare the thermostability of Bacillus licheniformis and Aspergillus niger α-amylase

Abstract

The thermostability of enzymes plays a significant role in the starch hydrolysis process in the industry. The structural difference between thermostable Bacillus licheniformis α-amylase (BLA) and thermolabile Aspergillus niger α-amylase (ANA) is interesting to be explored. This work aimed to study the thermostability-determining factor of BLA as compared to a non-thermostable enzyme, ANA, using molecular dynamics (MD) simulation at a high temperature. A 100 ns of classical MD, which was followed by 200 ns accelerated MD was conducted to explore the conformational changes of the enzyme. It is revealed that the intramolecular interactions through salt bridge interactions and the presence of calcium ions dominates the stability effect of BLA, despite the absence of a disulfide bond in the structure. These results should be useful in designing a thermostable enzyme that can be used in industrial processes.

Communicated by Ramaswamy H. Sarma

Keywords:

• α-Amylase
• thermostability
• accelerated molecular dynamics
• Bacillus licheniformis
• Aspergillus niger

Acknowledgement

We would also like to thank Professor Soetijoso Soemitro for his enlightening discussions about enzyme engineering.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

We want to thank Universitas Padjadjaran for their support of this work by the Internal Grant through Riset Kompetensi Dosen Unpad Funding [No. 2362/UN6.D/KS/2018] and the Academic Leadership Grant. Also, we acknowledge computing services supported by a PPTI Grant [No. 05/E/KPT/2018] from Ristekdikti.