In Silico Analysis of Relative Rareness, Codon Usage, and Enzymesubstrate Docking of Lampyroidea Maculata luciferase

Abstract

Aim: The purpose of this study was to conduct in silico analysis of the Lampyroidea maculata luciferase enzyme. Background: Bioluminescence is the production and emission of light by the luciferase enzymes in a living organism. The luciferase enzyme has been widely used in biotechnology due to its excellent properties. Objective: Recently, the new gene of the luciferase from the Lampyroidea maculata, has been cloned and characterized. Methods: In the following, in silico analysis of this enzyme were conducted by structural modeling in the I-TASSER web server. Finally, the binding site properties were studied using the AutoDock Vina. In the following, the codon usage bias parameters as the CAI, CBI, ENC, and the base composition of this sequence were studied. After analysis of the base composition, it was found that the coding DNA sequence is rich in AT. Moreover, the indices GC1, GC2, and GC3 were computed to establish the relationship among three codon positions. On the other hand, the GC2 has a much lower frequency. Results: By molecular modeling, some rare codons were identified that may have a critical role in the structure and function of this luciferase. The GC3% of the CDs was 17/304 and GC3 Skewness was 0.115. The GC content at the first codon position (GC1) and second codon position (GC2) was compared with that of the third codon position (GC3). AutoDock Vina was used in the molecular docking that recognizes some residues that yield closely related to the ADSL binding site. This bioinformatics analyzes play an important role in the design of new drugs. Conclusion: Previous studies show that mutation pressure and natural selection reasons for codon usage variation among different genes. If the mutational pressure was the only effective reason for the codon usage bias, then the frequency of nucleotides C and G should be equal to A and T at the synonymous third codon position. 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.