[1]
Ettensohn, C.E.; Wessel, G.M.; Wray, G. Development of sea urchins, ascidians, and other invertebrate deuterostomes: Experimental approaches, 1st ed; Academic Press, 2004, Vol. 74, p. 92.
[2]
Viviani, V.R. The origin, diversity, and structure function relationships of insect luciferases. Cell. Mol. Life Sci., 2002, 59(11), 1833-1850.
[3]
Wilson, T.; Hastings, J.W. Bioluminescence. Annu. Rev. Cell Dev. Biol., 1998, 14(1), 197-230.
[4]
Wood, K. The bioluminescence advantage. Promega Notes, 2007, 96, 3-5.
[5]
Ando, Y.; Niwa, K.; Yamada, N.; Enomoto, T.; Irie, T.; Kubota, H.; Ohmiya, Y.; Akiyama, H. Firefly bioluminescence quantum yield and colour change by pH-sensitive green emission. Nat. Photonics, 2008, 2(1), 44-47.
[6]
Bünzli, J.C.G.; Piguet, C. Taking advantage of luminescent lanthanide ions. Chem. Soc. Rev., 2005, 34(12), 1048-1077.
[7]
Hosseinkhani, S. Expression and purification of the luciferase enzyme and in vivo ATP assay. Physiol. Pharmacol., 2008, 12(2), 109-114.
[8]
Gould, S.J.; Subramani, S. Firefly luciferase as a tool in molecular and cell biology. Anal. Biochem., 1988, 175(1), 5-13.
[9]
Ronaghi, M.; Karamohamed, S.; Pettersson, B.; Uhlén, M.; Nyrén, P. Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem., 1996, 242(1), 84-89.
[10]
Kricka, L.J. Clinical and biochemical applications of luciferases and luciferins. Anal. Biochem., 1988, 175(1), 14-21.
[11]
Herschman, H.R. Noninvasive imaging of reporter gene expression in living subjects. Adv. Cancer Res., 2004, 92, 30-80.
[12]
White, P.; Squirrell, D.; Arnaud, P.; Lowe, C.; Murray, J. Improved thermostability of the North American firefly luciferase: saturation mutagenesis at position 354. Biochem. J., 1996, 319, 343-350.
[13]
Seliger, H.H.; McElroy, W.D. Spectral emission and quantum yield of firefly bioluminescence. Arch. Biochem. Biophys., 1960, 88(1), 136-141.
[14]
Seliger, H.; McElroy, W. The colors of firefly bioluminescence: Enzyme configuration and species specificity. Proc. Natl. Acad. Sci. USA, 1964, 52(1), 75.
[15]
Ueda, I.; Shinoda, F.; Kamaya, H. Temperature-dependent effects of high pressure on the bioluminescence of firefly luciferase. Biophys. J., 1994, 66(6), 2107-2110.
[16]
Haney, P.J.; Badger, J.H.; Buldak, G.L.; Reich, C.I.; Woese, C.R.; Olsen, G.J. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc. Natl. Acad. Sci., 1999, 96(7), 3578-3583.
[17]
Kumar, S.; Tsai, C.J.; Nussinov, R. Factors enhancing protein thermostability. Protein Eng., 2000, 13(3), 179-191.
[18]
Argos, P.; Rossmann, M.G.; Grau, U.M.; Zuber, H.; Frank, G.; Tratschin, J.D. Thermal stability and protein structure. Biochem., 1979, 18(25), 5698-5703.
[19]
Zhou, X.X.; Wang, Y.B.; Pan, Y.J.; Li, W.F. Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins. Amino Acids, 2008, 34(1), 25-33.
[20]
Catanzano, F.; Barone, G.; Graziano, G.; Capasso, S. Thermodynamic analysis of the effect of selective monodeamidation at asparagine 67 in ribonuclease A. Protein Sci., 1997, 6(8), 1682-1693.
[21]
Chakravarty, S.; Varadarajan, R. Elucidation of determinants of protein stability through genome sequence analysis. FEBS Lett., 2000, 470(1), 65-69.
[22]
Pack, S.P.; Yoo, Y.J. Packing-based difference of structural features between thermophilic and mesophilic proteins. Int. J. Biol. Macromol., 2005, 35(3-4), 169-174.
[23]
Dill, K.A. Dominant forces in protein folding. Biochem., 1990, 29(31), 7133-7155.
[24]
Vogt, G.; Woell, S.; Argos, P. Protein thermal stability, hydrogen bonds, and ion pairs. J. Mol. Biol., 1997, 269(4), 631-643.
[25]
Sadeghi, M.; Naderi-Manesh, H.; Zarrabi, M.; Ranjbar, B. Effective factors in thermostability of thermophilic proteins. Biophys. Chem., 2006, 119(3), 256-270.
[26]
Xiao, L.; Honig, B. Electrostatic contributions to the stability of hyperthermophilic proteins. J. Mol. Biol., 1999, 289(5), 1435-1444.
[27]
Mrabet, N.T.; Van den Broeck, A.; Van den Brande, I.; Stanssens, P.; Laroche, Y.; Lambeir, A.M.; Matthijssens, G.; Jenkins, J.; Chiadmi, M. Arginine residues as stabilizing elements in proteins. Biochem., 1992, 31(8), 2239-2253.
[28]
Mortazavi, M.; Hosseinkhani, S. Design of thermostable luciferases through arginine saturation in solvent-exposed loops. Protein Eng. Des. Sel., 2011, 24(12), 893-903.
[29]
Mortazavi, M.; Hosseinkhani, S. Surface charge modification increases firefly luciferase rigidity without alteration in bioluminescence spectra. Enzyme Microb. Technol., 2017, 96, 47-59.
[30]
Kaplan, W.; Littlejohn, T.G. Swiss-PDB viewer (deep view). Brief. Bioinform., 2001, 2(2), 195-197.
[31]
DeLano, W.L. The PyMOL molecular graphics system. Delano Sci., San Carlos, 2002, 7(1)
[32]
Kheirabadi, M.; Sharafian, Z.; Naderi-Manesh, H.; Heineman, U.; Gohlke, U.; Hosseinkhani, S. Crystal structure of native and a mutant of Lampyris turkestanicus luciferase implicate in bioluminescence color shift. Biochim. Biophys. Acta. Proteins Proteomics, 2013, 1834(12), 2729-2735.
[33]
Wang, W.; Malcolm, B. Two-stage PCR protocol allowing introduction of multiple mutations, deletions and insertions using quikchange site-directed mutagenesis. Biotech., 1999, 26(4), 680-682.
[34]
Mortazavi, M.; Hosseinkhani, S.; Khajeh, K.; Ranjbar, B.; Emamzadeh, A.R. Spectroscopic and functional characterization of Lampyris turkestanicus luciferase: A comparative study. Acta Biochim. Biophys. Sin., 2008, 40(5), 365-374.
[35]
Bradford, M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem., 1976, 72(1-2), 248-254.
[36]
Alipour, B.S.; Hosseinkhani, S.; Ardestani, S.K.; Moradi, A. The effective role of positive charge saturation in bioluminescence color and thermostability of firefly luciferase. Photochem. Photobiol. Sci., 2009, 8(6), 847-855.
[37]
Yousefi, F.; Ataei, F.; Mortazavi, M.; Hosseinkhani, S. Bifunctional role of leucine 300 of firefly luciferase in structural rigidity. Int. J. Biol. Macromol., 2017, 101, 67-74.
[38]
Emamzadeh, A.R.; Hosseinkhani, S.; Sadeghizadeh, M.; Nikkhah, M.; Chaichi, M.J.; Mortazavi, M. cDNA cloning, expression and homology modeling of a luciferase from the firefly Lampyroidea maculata. BMB Rep., 2006, 39(5), 578-585.
[39]
Hosseinkhani, S.; Szittner, R.; Meighen, E. Random mutagenesis of bacterial luciferase: Critical role of Glu175 in the control of luminescence decay. Biochem. J., 2005, 385, 575-580.
[40]
Eftink, M.; Ghiron, C. Exposure of tryptophanyl residues and protein dynamics. Biochemistry, 1977, 16(25), 5546-5551.
[41]
Schwede, T.; Kopp, J.; Guex, N.; Peitsch, M.C. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res., 2003, 31(13), 3381-3385.
[42]
Zhang, Y. I-Tasser server for protein 3D structure prediction. BMC BioI., 2008, 9(1), 40.
[43]
Tina, K.; Bhadra, R.; Srinivasan, N. PIC: Protein Interactions Calculator. Nucleic Acids Res., 2007, 35(Web Server issue), W473-W476.
[44]
Guex, N.; Peitsch, M. Swiss-PdbViewer: A fast and easy-to-use PDB viewer for Macintosh and PC. Protein Data Bank Quat. Newslett, 1996, 77(7)
[45]
Vriend, G. What If: A molecular modeling and drug design program. J. Mol. Graph., 1990, 8(1), 52-56.
[46]
Snider, C.; Jayasinghe, S.; Hristova, K.; White, S.H. MPEx: A tool for exploring membrane proteins. Protein Sci., 2009, 18(12), 2624-2628.
[47]
Yousefi-Nejad, M.; Hosseinkhani, S.; Khajeh, K.; Ranjbar, B. Expression, purification and immobilization of firefly luciferase on alkyl-substituted Sepharose 4B. Enzyme Microb. Technol., 2007, 40(4), 740-746.
[48]
LE1-IRER. S. Solute perturbation of protein fluorescence. The quenching of tryptophyl fluorescence of model compounds and of lysozyme by iodide ion. Biochem., 1971, 10, 3254-3263.
[49]
Lehrer, S. The selective quenching of tryptophan fluorescence in proteins by iodide ion: lysozyme in the presence and absence of substrate. Biochem. Biophys. Res. Commun., 1967, 29(5), 767-772.
[50]
Emamzadeh, R.; Hosseinkhani, S.; Hemati, R.; Sadeghizadeh, M. RACE-based amplification of cDNA and expression of a Luciferin-Regenerating Enzyme (LRE): an attempt towards persistent bioluminescent signal. Enzyme Microb. Technol., 2010, 47(4), 159-165.
[51]
Gomi, K.; Hirokawa, K.; Kajiyama, N. Molecular cloning and expression of the cDNAs encoding luciferin-regenerating enzyme from Luciola cruciata and Luciola lateralis. Gene, 2002, 294(1), 157-166.
[52]
Hosseinkhani, S. Molecular enigma of multicolor bioluminescence of firefly luciferase. Cell. Mol. Life Sci., 2011, 68(7), 1167-1182.
[53]
Strub, C.; Alies, C.; Lougarre, A.; Ladurantie, C.; Czaplicki, J.; Fournier, D. Mutation of exposed hydrophobic amino acids to arginine to increase protein stability. BMC Biochem., 2004, 5(1), 9.
[54]
Tafreshi, N.K.; Hosseinkhani, S.; Sadeghizadeh, M.; Sadeghi, M.; Ranjbar, B.; Naderi-Manesh, H. The influence of insertion of a critical residue (Arg356) in structure and bioluminescence spectra of firefly luciferase. J. Biol. Chem., 2007, 282(12), 8641-8647.
[55]
Nowroozi-Nejad, Z.; Bahramian, B.; Hosseinkhani, S. Efficient immobilization of firefly luciferase in a metal organic framework: Fe-MIL-88 (NH2) as a mighty support for this purpose. Enzyme Microb. Technol., 2019, 121, 59-67.
[56]
Chu, Y.; Hou, J.; Boyer, C.; Richardson, J.J.; Liang, K.; Xu, J. Biomimetic synthesis of coordination network materials: Recent advances in MOFs and MPNs. Appl. Mater. Today, 2018, 10, 93-105.
[57]
Fattahi, M.; Malekpour, A.; Mortazavi, M.; Safarpour, A.; Naseri, N. The characteristics of rare codon clusters in the genome and proteins of hepatitis C virus; a bioinformatics look. Middle East J. Dig. Dis., 2014, 6(4), 214.
[58]
Ghorban, H.N.; Tebianian, M.; Farhadi, A.; Hossein, K.A.; Rahimi, A.; Mortazavi, M.; Hosseini, S.Y.; Taghizadeh, M.; Rezaei, M.; Mahdavi, M. In silico analysis of L1/L2 sequences of human papillomaviruses: implication for universal vaccine design. Viral Immunol., 2017, 30(3), 210-223.
[59]
Mortazavi, M.; Zarenezhad, M.; Alavian, S.M.; Gholamzadeh, S.; Malekpour, A.; Ghorbani, M.; Mahani, M.T.; Lotfi, S.; Fakhrzad, A. Bioinformatics analysis of codon usage and phylogenetic relationships in different genotypes of the hepatitis C virus. Hepat. Mon., 2016, 16(10)e39196
[60]
Kargar, F.; Mortazavi, M.; Savardashtaki, A.; Hosseinkhani, S.; Mahani, M.T.; Ghasemi, Y. Genomic and protein structure analysis of the luciferase from the Iranian bioluminescent beetle, Luciola sp. Int. J. Biol. Macromol., 2019, 124, 689-698.
[61]
Mortazavi, M.; Zarenezhad, M.; Gholamzadeh, S.; Alavian, S.M.; Ghorbani, M.; Dehghani, R.; Malekpour, A.; Meshkibaf, M.; Fakhrzad, A. Bioinformatics identification of rare codon clusters (RCCs) in HBV genome and evaluation of RCCs in proteins structure of hepatitis B virus. Hepat. Mon., 2016, 16(10)e39909
[62]
Mortazavi, M.; Nezafat, N.; Negahdaripour, M.; Gholami, A.; Torkzadeh-Mahani, M.; Lotfi, S.; Ghasemi, Y. In silico evaluation of rare codons and their positions in the structure of cytosine deaminase and substrate docking studies. Trends Pharmacol. Sci., 2016, 2(2), 117-130.
[63]
Malekpour, A.; Mortazavi, M.; Elyadrani, K.E.; Zahedi, S.; Ghorbani, M. Bioinformatics analysis of codon usage and phylogenetic relationships of different genotypes of hepatitis C virus: p23. J. Viral Hepat., 2015, 22, 33-34.
[64]
Daniel, E.; Weber, G. Cooperative effects in binding by bovine serum albumin. I. The binding of 1-anilino-8-naphthalenesulfonate. Fluorimetric titrations. Biochemistry, 1966, 5(6), 1893-1900.
[65]
Steinberg, I.Z. Long-range nonradiative transfer of electronic excitation energy in proteins and polypeptides. Annu. Rev. Biochem., 1971, 40(1), 83-114.