Molecular docking and bioinformatics study of rare codons in the Lampyroidea maculata luciferase gene

Mortazavi, Mojtaba; Torkzadeh-Mahani, Masoud; Hosseinkhani, Saman; Lotfi, Safa; Rahman, Emamzadeh

Molecular docking and bioinformatics study of rare codons in the Lampyroidea maculata luciferase gene

Document Type : Original Research

Authors

Mojtaba Mortazavi ¹

Masoud Torkzadeh-Mahani ¹

Saman Hosseinkhani ²

Safa lotfi ¹

Emamzadeh Rahman ³

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

² Department of Biochemistry, Faculty of Basic Sciences, Tarbiat Modares University, Tehran, Iran

³ Department of Biology Faculty of Sciences University of Isfahan

Abstract

The bioluminescence process is a widespread phenomenon in Nature. These enzymes are identified in some domains of life, but the luciferases from the lampyridea genus are considered for biological applications. The molecular cloning of a new type of Iranian firefly luciferase from Lampyroidea maculata was reported, previously. In this study, we analyzed the rare codons of the Iranian insect luciferase gene using the computational databases as ATGme, RACC, LaTcOm, and Sherlocc. Also, the structural modeling process of this enzyme was performed. Next, the status of these rare codons in this structural 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 luciferase. AutoDock Vina was used in the molecular docking that recognizes Asp⁵³¹that yield closely related to luciferin and AMP binding site.. This bioinformatics analyzes play an important role in the design of new drugs.

Keywords

Lampyroidea maculata

Luciferase

rare codon

substrate binding site

20.1001.1.23222115.1399.11.2.1.2

Subjects

Bioinformatics

1. Denburg JL, Lee RT, McElroy W. Substrate-binding properties of firefly luciferase: I. Luciferin-binding site. Archives of biochemistry and biophysics 1969;134:381-394.
2. DeLuca M, McElroy WD. Kinetics of the firefly luciferase catalyzed reactions. Biochemistry 1974;13:921-925.
3. White EH, Rapaport E, Seliger HH, Hopkins TA. The chemi-and bioluminescence of firefly luciferin: an efficient chemical production of electronically excited states. Bioorganic Chemistry 1971;1:92-122.
4. Viviani V. The origin, diversity, and structure function relationships of insect luciferases. Cellular and Molecular Life Sciences CMLS 2002;59:1833-1850.
5. Alipour BS, Hosseinkhani S, Nikkhah M, Naderi-Manesh H, Chaichi MJ, Osaloo SK. Molecular cloning, sequence analysis, and expression of a cDNA encoding the luciferase from the glow-worm, Lampyris turkestanicus. Biochemical and biophysical research communications 2004;325:215-222.
6. Mortazavi M, Hosseinkhani S. Surface charge modification increases firefly luciferase rigidity without alteration in bioluminescence spectra. Enzyme and microbial technology 2017;96:47-59.
7. Emamzadeh AR, Hosseinkhani S, Sadeghizadeh M, Nikkhah M, Chaichi MJ, Mortazavi M. cDNA cloning, expression and homology modeling of a luciferase from the firefly Lampyroidea maculata. BMB Reports 2006;39:578-585.
8. Hosseinkhani S. Molecular enigma of multicolor bioluminescence of firefly luciferase. Cellular and Molecular Life Sciences 2011;68:1167-1182.
9. Branchini BR, Magyar RA, Murtiashaw MH, Anderson SM, Helgerson LC, Zimmer M. Site-directed mutagenesis of firefly luciferase active site amino acids: a proposed model for bioluminescence color. Biochemistry 1999;38:13223-13230.
10. Lundin A. Use of firefly luciferase in ATP-related assays of biomass, enzymes, and metabolites. Methods in enzymology 2000;305:346-370.
11. Dix DB, Thompson RC. Codon choice and gene expression: synonymous codons differ in translational accuracy. Proceedings of the National Academy of Sciences 1989;86:6888-6892.
12. Chartier M, Gaudreault F, Najmanovich R. Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events. Bioinformatics 2012;28:1438-1445.
13. Widmann M, Clairo M, Dippon J, Pleiss J. Analysis of the distribution of functionally relevant rare codons. BMC genomics 2008;9:207.
14. Kypr J. A part of codon bias in genes protects protein spatial structures from destabilization by random single point mutations. Biochemical and biophysical research communications 1986;139:1094-1097.
15. Daniel E, Onwukwe GU, Wierenga RK, Quaggin SE, Vainio SJ, Krause M. ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization. BMC bioinformatics 2015;16:303.
16. Theodosiou A, Promponas VJ. LaTcOm: a web server for visualizing rare codon clusters in coding sequences. Bioinformatics 2012;28:591-592.
17. Thanaraj T, Argos P. Protein secondary structural types are differentially coded on messenger RNA. Protein science 1996;5:1973-1983.
18. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997;18:2714-2723.
19. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC bioinformatics 2008;9:40.
20. Kaplan W, Littlejohn TG. Swiss-PDB viewer (deep view). Briefings in bioinformatics 2001;2:195-197.
21. DeLano WL. The PyMOL molecular graphics system. 2002.
22. Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry 2010;31:455-461.
23. Wu S, Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic acids research 2007;35:3375-3382.
24. Nakatsu T, Ichiyama S, Hiratake J, Saldanha A, Kobashi N, Sakata K, Kato H. Structural basis for the spectral difference in luciferase bioluminescence. Nature 2006;440:372.
25. Franks N, Jenkins A, Conti E, Lieb W, Brick P. Structural basis for the inhibition of firefly luciferase by a general anesthetic. Biophysical journal 1998;75:2205-2211.
26. Vriend G. WHAT IF: a molecular modeling and drug design program. Journal of molecular graphics 1990;8:52-56.
27. Tina K, Bhadra R, Srinivasan N. PIC: protein interactions calculator. Nucleic acids research 2007;35:W473-W476.
28. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of computational chemistry 2009;30:2785-2791.
29. O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. Journal of cheminformatics 2011;3:33.
30. Dong H, Nilsson L, Kurland CG. Co-variation of trna abundance and codon usage inescherichia coliat different growth rates. Journal of molecular biology 1996;260:649-663.
31. Clarke IV TF, Clark PL. Rare codons cluster. PloS one 2008;3:e3412.
32. Wood KV. Luc genes: introduction of colour into bioluminescence assays. Journal of bioluminescence and chemiluminescence 1990;5:107-114.
33. Fan F, Wood KV. Bioluminescent assays for high-throughput screening. Assay and drug development technologies 2007;5:127-136.
34. Meisenheimer PL, O’BRIEN MA, Cali JJ. Luminogenic enzyme substrates: The basis for a new paradigm in assay design. EDITOR’S DESK 2008.
35. Greer LF, Szalay AA. Imaging of light emission from the expression of luciferases in living cells and organisms: a review. Luminescence 2002;17:43-74.
36. Lyons SK, Meuwissen R, Krimpenfort P, Berns A. The generation of a conditional reporter that enables bioluminescence imaging of Cre/loxP-dependent tumorigenesis in mice. Cancer Research 2003;63:7042-7046.
37. Gabriel GV, Viviani VR. Novel application of pH-sensitive firefly luciferases as dual reporter genes for simultaneous ratiometric analysis of intracellular pH and gene expression/location. Photochemical & Photobiological Sciences 2014;13:1661-1670.
38. Mortazavi M, Zarenezhad M, Gholamzadeh S, Alavian SM, Ghorbani M, Dehghani R, Malekpour A, et al. Bioinformatic Identification of Rare Codon Clusters (RCCs) in HBV Genome and Evaluation of RCCs in Proteins Structure of Hepatitis B Virus. Hepatitis Monthly 2016;16.
39. Varenne S, Baty D, Verheij H, Shire D, Lazdunski C. The maximum rate of gene expression is dependent in the downstream context of unfavourable codons. Biochimie 1989;71:1221-1229.
40. Zhang G, Ignatova Z. Generic algorithm to predict the speed of translational elongation: implications for protein biogenesis. PloS one 2009;4:e5036.
41. Novoa EM, de Pouplana LR. Speeding with control: codon usage, tRNAs, and ribosomes. Trends in Genetics 2012;28:574-581.
42. Kane JF. Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Current opinion in biotechnology 1995;6:494-500.
43. Komar AA, Lesnik T, Reiss C. Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation. FEBS letters 1999;462:387-391.
44. Overton TW. Recombinant protein production in bacterial hosts. Drug discovery today 2014;19:590-601.
45. Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein engineering 1995;8:127-134.
46. Sundlov JA, Fontaine DM, Southworth TL, Branchini BR, Gulick AM. Crystal structure of firefly luciferase in a second catalytic conformation supports a domain alternation mechanism. Biochemistry 2012;51:6493-6495.
47. Leaf-nosed bat. In: Encyclopædia Britannica: Encyclopædia Britannica Online; 2009.
48. Mortezavi M, Torkzadeh-Mahani M, Nezafat N, Malekpour A, Zarenezhad M, Hemmati R, Maleki M, et al. Molecular Docking and Rare Codons Evaluation in the Luciola Lateralis luciferase, an in Silico Study. Biomacromolecular Journal 2017;3:48-59.
49. Auld DS, Lovell S, Thorne N, Lea WA, Maloney DJ, Shen M, Rai G, et al. Molecular basis for the high-affinity binding and stabilization of firefly luciferase by PTC124. Proceedings of the National Academy of Sciences 2010;107:4878-4883.