Document Type : Research Paper

Authors

• mojtaba mortazavi ¹
• Masoud Torkzadeh-Mahani ¹
• Mehdi Rahimi ¹
• Ali Riahi-Madvar ²

¹ 1Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran;

² Department of Molecular and Cell Biology, Faculty of Basic Sciences, Kosar University of Bojnord, Bojnord, Iran.

Abstract

Luciferases are enzymes that are involved in the emission of light are widely used in the field of industrial and medical biotechnology. We previously reported the cloning of the luciferase gene from the Iranian firefly, Luciola sp. Using computational methods, we analyzed the hidden layer of genetic and structural data in the Luciola sp. For this, with the help of ACUA software, the ENC and CBI were studied and the AT1, GC1, AT2, GC2, AT3, and GC3 contents were calculated. In the following, the UNAFold and Mfold Servers were used to predict RNA folding. The 3D model analysis and ChExVis method was used for extracting, storing, and analyzing luciferase channels. Finally, in silico substrate docking was conducted in the AutoDock Vina. The GC3 Skewness and GC3% of the cds were calculated as 0.39 and 17.153, respectively. This analysis shows that there are some rare codons of Pro, Arg, Ile, and Leu. The docking of 5'-O-[N-(Dehydroluciferyl)-sulfamoyl]-adenosine with luciferase was conducted and a network of interactions was identified. In the RNAfold applet, the best secondary structure has a free energy of -397.70 kcal/mol and the thermodynamic free energy is -427.28 kcal/mol. In the ensemble, the frequency of the MFE structure is 0.00 % and the diversity of the ensemble is 477.94. In this study, some hidden biological information from the genetic code was identified which may have a function in the proper folding and substrate-binding site and show that codon compositions may have roles in the proper folding of this enzyme.

Keywords

• luciferase
• Docking
• rare codon
• RNA folding
• AutoDock Vina

Main Subjects

• Biochemistry