In Silico study of 1, 4 alpha Glucan Branching Enzyme and Substrate Docking Studies

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

Journal Name: Current Proteomics

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Abstract:

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

Method: For a better evaluation, the important characteristics of this enzyme 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) was 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 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 of the sequence and structure of this enzyme was created, and our findings can be used in some fields of the clinical and industrial biotechnology.

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

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(E-pub Ahead of Print)
DOI: 10.2174/1570164616666190401204009
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