Title:In Silico Analysis of Relative Rareness, Codon Usage, and Enzymesubstrate Docking of Lampyroidea Maculata luciferase
Volume: 18
Issue: 3
Author(s): Mojtaba Mortazavi*, Saman Hosseinkhani, Masoud Torkzadeh-Mahani, Safa Lotfi, Rahman Emamzadeh and Younes Ghasemi
Affiliation:
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman,Iran
Keywords:
Lampyroidea maculata, luciferase, CAI, CBI, ENC, rare codon, autoDock vina, codon usage.
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.