In Silico Study of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies

Author(s): Farzane Kargar, Amir Savardashtaki*, Mojtaba Mortazavi*, Masoud Torkzadeh Mahani, Ali Mohammad Amani, Younes Ghasemi, Navid Nezafat

Journal Name: Current Proteomics

Volume 17 , Issue 1 , 2020

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Abstract:

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server.

Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina.

Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence.

Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.

Keywords: Neisseria, molecular modeling, phylogenetic tree, bioinformatics, AutoDock Vina, glucan.

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VOLUME: 17
ISSUE: 1
Year: 2020
Page: [40 - 50]
Pages: 11
DOI: 10.2174/1570164616666190401204009
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