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In silico analysis of relative rareness, codon usage, and enzyme-substrate docking of Lampyroidea maculata luciferase

Author(s):

Mojtaba Mortazavi*, Saman Hosseinkhani, Masoud Torkzadeh-Mahani, Safa Lotfi, Rahman Emamzadeh and Younes Ghasemi   Pages 1 - 12 ( 12 )

Abstract:


Bioluminescence is the production and emission of light by the luciferase enzymes in a living organism. The luciferases were identified in different domains of life, but the Lampyridae luciferases are considered for biotechnological and clinical applications. Recently, the new Iranian luciferase gene from the Lampyroidea maculata has been cloned and characterized. In this study, in silico analysis of this enzyme as the codon usage bias parameters (CAI, CBI, ENC, and rare codons) were conducted. Furthermore, the 3D structure of this enzyme was modeled in the I-TASSER web server and the status of these rare codons in this model was studied using SPDBV and PyMOL software. In the following, the substrate-binding site was studied using the AutoDock Vina. By molecular modeling, some rare codons were identified that may have a critical role in the structure and function of this enzyme. The GC3% of the CDs was 17/304 and GC3 Skewness was 0.115. The molecular docking analysis recognizes some residues that yield closely related to the DLSA binding site. 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 clinical and industrial biotechnology. This bioinformatics analysis plays an important role in the design of the new recombinant enzyme.

Keywords:

Lampyroidea maculata, luciferase, CAI, CBI, ENC, rare codon, AutoDock Vina, codon usage

Affiliation:

Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Department of Biochemistry, Faculty of Basic Sciences, Tarbiat Modares University, Tehran, Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Department of Biology Faculty of Sciences University of Isfahan, Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies Shiraz University of Medical Sciences Shiraz



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