Biopolym. Cell. 2007; 23(2):130-136.
http://dx.doi.org/10.7124/bc.00075F
Molecular Biophysics
Conformational mobility investigation of tyrosyl-tRNA synthetase C-module and its complex with tRNA using the methods of time-resolved fluorescence spectroscopy
1Kordysh M. O., 1Kyryushko G. V., 2Mely Y., 1Kornelyuk O. I.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
  2. Universite de Strasbourg
    4, rue Blaise Pascal, Strasbourg, France, F-67081

Abstract

The non-catalytic C-module of mammalian tyrosyl-tRNA synthetase displays both RNA-binding ability and cytokine activity. C-module contains a unique tryptophan residue (Trpl44), located out of RNA-binding site and a conservative aromatic residue Phe127 located inside of its RNA-binding site. Phe127 was replaced by fluorophore Trp 127 using the method of site-directed mutagenesis. The interaction of C-module with tRNA was investigated by time-resolved fluorescence spectroscopy. Obtained fluorescence decay parameters of Trp144 and Trp127 of C-module and its complex with tRNA are characterized by the additional short-lived component without any significant changing of other fluorescence parameters in the presence of nucleic acid. These data indicate the existence of the polymorphism of Trp 127 microenvironment that is conditioned by the dynamic protein-nucleic acid interaction mechanism.
Keywords: tyrosyl-tRNA synthetase C-module, time-resolved fluorescence spectroscopy, conformational mobility.
Full text: (PDF, in English) (PDF, in Ukrainian)

References

[1] Kornelyuk AI, Tas MPR, Dubrovsky AL, Murray JC. Cytokine activity of the non-catalytic EMAP-2-like domain of mammalian tyrosyl-tRNA synthetase. Biopolym Cell. 1999; 15(2):168-72.
[2] Wakasugi K, Schimmel P. Two distinct cytokines released from a human aminoacyl-tRNA synthetase. Science. 1999;284(5411):147-51.
[3] Kordysh MA, Odynets KA, Kornelyuk AI. Trp144 as a fluorescence probe for investigation of the C-module rapid conformation dynamics in eukaryotic tyrosyle-tRNA synthetase. Biopolym Cell. 2003; 19(5):436-9.
[4] Kordysh MA, Kornelyuk AI. The monitoring of conformational changes of the Trp144 residue environment in C-module of tyrosyl-tRNA synthetase undr heat denaturation. Dopovidi Nats Akad Nauk Ukrainy. 2004; (1):156-61.
[5] Kordysh M, Kornelyuk A. Conformational flexibility of cytokine-like C-module of tyrosyl-tRNA synthetase monitored by Trp144 intrinsic fluorescence. J Fluoresc. 2006;16(5):705-11.
[6] Kordysh MA, Kornelyuk AI. Investigation of the interaction between isolated C-module of tyrosyl-tRNA synthetase and tRNA by fluorescence spectroscopy. Biopolym Cell. 2006;22(4):283-9.
[7] Simos G, Segref A, Fasiolo F, Hellmuth K, Shevchenko A, Mann M, Hurt EC. The yeast protein Arc1p binds to tRNA and functions as a cofactor for the methionyl- and glutamyl-tRNA synthetases. EMBO J. 1996;15(19):5437-48.
[8] Kushiro T, Schimmel P. Trbp111 selectively binds a noncovalently assembled tRNA-like structure. Proc Natl Acad Sci U S A. 2002;99(26):16631-5.
[9] Shalak V, Kaminska M, Mitnacht-Kraus R, Vandenabeele P, Clauss M, Mirande M. The EMAPII cytokine is released from the mammalian multisynthetase complex after cleavage of its p43/proEMAPII component. J Biol Chem. 2001;276(26):23769-76.
[10] Murzin AG. OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J. 1993;12(3):861-7.
[11] Livesey AK, Brochon JC. Analyzing the distribution of decay constants in pulse-fluorimetry using the maximum entropy method. Biophys J. 1987;52(5):693-706.
[12] Lakowicz J. R. Principles of fluorescent spectroscopy. New York: Plenum press, 1999. 698 p.
[13] Kanibolotskiy DS, Odynets KA, Skurskiy SI, Kornelyuk AI. Study of intramolecular mobility of cytokine-like C-terminal module of tyrosyl-mammalian tRNA synthetase by molecular dynamics. Physics live. 2003; 11(2):61-71.
[14] Chen Y, Liu B, Yu H-T, Barkley MD. The peptide bond quenches indole fluorescence. J Am Chem Soc. 1996;118(39):9271–8.
[15] Chen Y, Barkley MD. Toward understanding tryptophan fluorescence in proteins. Biochemistry. 1998;37(28):9976-82.
[16] McMahon LP, Yu H-T, Vela MA, Morales GA, Shui L, Fronczek FR, et al. Conformer interconversion in the excited state of constrained tryptophan derivatives. J Phys Chem B. 1997;101(16):3269–80.
[17] Sillen A, Hennecke J, Roethlisberger D, Glockshuber R, Engelborghs Y. Fluorescence quenching in the DsbA protein from Escherichia coli: complete picture of the excited-state energy pathway and evidence for the reshuffling dynamics of the microstates of tryptophan. Proteins. 1999;37(2):253-63.