Department of Protein Synthesis Enzymology
Mykhailo A. Tukalo
Professor, Dr. Sci. (Mol. Biol.),
Laboratory of Instrumental Research Methods
Head - Iryna O. Blyum
Head: Zenoviy Yu. Tkachuk
Head: Maria Yu. Obolens'ka
Education and Degrees:
1968–1973 Graduate Student, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine, M.Sc. (biochemistry)
1981 Ph.D. (molecular biology)
1989 Dr.Sci. (molecular biology)
2005 Professor, Taras Shevchenko National University of Kyiv
2009 Corresponding Member of NASU
2018 Member of National Academy of Sciences of Ukraine
1973 Research Assistant, Institute of Molecular Biology and Genetics (IMBG), NASU, Kyiv, Ukraine (molecular biology)
1974–1977 Visiting Scientist at the Novosibirsk Institute of Bioorganic Chemistry, Novosibirsk, Russia
1977–1982 Junior Research Scientist, Group leader, IMBG NASU, Kyiv, Ukraine
1982–1986 Senior Research Scientist, Group leader, IMBG NASU, Kyiv, Ukraine
1986–1990 Leading Research Scientist, Group leader, IMBG NASU, Kyiv, Ukraine
since 1990 Head of the Department of Protein Synthesis Enzymology, IMBG NASU, Kyiv, Ukraine
1994–2002 Staff Scientist at the European Molecular Biology Laboratory, Grenoble Outstation, France
2006-2019 Deputy Director in Scientific Work, IMBG NASU, Kyiv, Ukraine
since 2019 - Director, Institute of Molecular Biology and Genetics (IMBG), NASU, Kyiv, Ukraine
Honours, Prizes, Awards:
1982 Medal “In memory of the 1500 anniversary of the city of Kyiv”
1986 State Prize of Ukraine in Science and Technology for contribution to molecular biology through research on the regulation of protein biosynthesis
1995–2000 Howard Hughes Medical Institute International Research Grant INTAS Collaborative Grant
2011 Diploma of Verhovna Rada of Ukraine
2011 Gershenson Award of National Academy of Sciences of Ukraine
Study on the molecular basis of decoding genetic information, translation quality control and RNA-protein recognition
Сurrent Research Activities and Recent Achievements:
Structural and functional study on aminoacyl-tRNA synthetases.
The research of the last years was directed at the identification of the structural bases of the decoding of genetic information. The current area is the specific recognition of aminoacyl-tRNA synthetases (aaRSs) for their cognate amino acid and tRNA, mechanisms of catalysis and editing. Using biochemical methods, site-directed mutagenesis and X-ray crystallography, a work was carried out on different prokaryotic (including important pathogenic bacteria Enterococcus faecalis, Mycobacterium tuberculosis and Streptococcus pneumoniae), eukaryotic and archaeal systems. In collaboration with Dr. S. Cusack (the European Molecular Biological Laboratory) the 3-dimensional structures of several aaRSs and their complexes with various combinations of substrata, including the tRNA complexes, are being studied. The synthesis of specific products by aaRSs has been shown to be accompanied by the conformational changes both in the active centre of enzyme and beyond. The data obtained allowed the understanding of the mechanism of amino acids activation and the molecular mechanism of the recognition of homologous tRNA and their aminoacylation by these enzymes.
Recognition of tRNAs with a long variable arm by aminoacyl-tRNA synthetases.
In prokaryotic cells three tRNA species, tRNASer, tRNATyr and tRNALeu, possess a long variable arm of 11–20 nucleotides (a type 2 tRNAs) rather than the usual 4 or 6 ( a type 1 tRNAs). We studied the molecular basis for recognition and discrimination of type 2 tRNAs by Thermus thermophilus seryl-, tyrosyl- and leucyl- tRNA synthetases (SerRS, TyrRS and LeuRS) using X-ray crystallography and chemical probing of tRNA in solution. The determination of a complex of SerRs and tRNASer provided the first information on the structure of a tRNA with a long variable arm and elucidated the details of how enzyme interacts with tRNA. As a result of solving the structure of TyrRS an unusual for these enzymes type recognition of tRNA has been demonstrated for the first time. Tyrosyl-tRNA synthetase belongs to the first structural class, but its type of recognition is specific for the class 2 aaRSs, where tRNA interacts with an enzyme from the side of a long variable arm. Finally, after the structure of a complex of the leucyl-tRNA synthetase with tRNALeu was determined, a full picture of the interaction of the synthetases with tRNA, which has a long variable arm, has been obtained. The distinctions, revealed in the tertiary structures of tRNASer, tRNATyr and tRNALeu, using the methods of X-ray structure analysis and chemical modification, allowed us to understand the importance of their role in the recognition and discrimination by homologous aaRSs.
The molecular basis for editing errors by aminoacyl-tRNA syntetases.
The affinity difference is not enough for the aminoacyltRNA synthetases to discriminate strictly between similar amino acids. When a tRNA is acylated with the wrong amino acid this would lead to an error in the incorporation of genetically coded amino acids into protein. To overcome this problem, several aaRSs have developed the ability to hydrolyze the mischarged tRNA in an extra editing domain. We are studying the molecular mechanisms of editing by synthetases from two different classes: Thermus thermophilus leucyltRNA leucyltRNA synthetase (LeuRSTT) from class I and Enterococcus fecalis prolyl-tRNA synthetase (ProRSEF) from class II. To understand the mechanisms of editing reaction for enzymes with absolutely different architecture of editing domains, we have used a number of approaches, including molecular modeling, quantum-mechanical calculations, site-directed mutagenesis and enzyme modification of tRNA. Our intensive alanine scanning mutagenesis of LeuRSTT and ProRSEF editing sites has failed to identify catalytic residues for hydrolysis within the active site. On the other hand, modification of tRNAPro at the 2’-OH of A76 and tRNALeu at the 3’-OH of A76 by replacing each of them with a hydrogen or fluorine, revealed an essential function of these groups in hydrolysis. On the basis of obtained experimental results and our QM/ MM calculations we suggest a tRNA-assisted mechanism of post-transfer editing by LeuRS and ProRS in which 2’- or 3’-OH group of the substrate plays a key role.
Development of novel classes of antibiotics.
We are using the differences between human and prokaryotic prolyl-, tyrosyl- and leucyl-tRNA synthetases for the development of the inhibitors as potential drugs against Mycobacterium tuberculosis, Enterococcus faecalis and Streptococcus pneumonia. The search strategy for antibacterial compounds is based on the combination of X-ray structural analysis of the target protein, computer modelling of the interaction of low-molecular ligands with the target protein and synthetic procedures of combinatorial chemistry.
Projects of National Academy of Sciences of Ukraine:
- 2012–2016 Progect: “Target-directed search for a new antibacterial, antiviral and antitumor agents” (scientific supervisor – M. Tukalo)
- 2010–2014 N 30/10 Progect: “Development of targetspecific technologies for searching of the aminoacyltRNA synthetases inhibitors with selective action against causative agents of human infection diseases” (scientific supervisor – M. Tukalo)
Projects of State Agency on Science, Innovations and Informatization of Ukraine:
- 2012 N 059/514 Project: "Development and application of target oriented methods for initial screening of molecules as potencial antibacterial agents". State registration No 0112U007642. The contract PR 059/514 13 .11. 2012 with the Kiev National University Т. Shevchenko (scientific supervisor – M. Tukalo).
- 2013–2016 GDRI (International Research Networks) Project: “From molecular to cellular events in human pathologies” (scientific supervisors – Prof. P. Curmi and Prof. O. Lavrik )
- 2011–2014 7th Framework Programme (FP7) FP7- INCO-2011-6, ERA-WIDE Project: “Strengthening cooperation in Molecular Biomedicine between EU and UKRAINE”, COMBIOM (scientific supervisor – Prof. A. Elskaya)
- 2011–2012 STCU (Science and Technology Center in Ukraine) Research Grants
- 2007–2009 STCU Research Grants
- 2001-2003 INTAS Collaborative Research Grant
- 1995-2000 Howard Hughes Medical Institute International Research Grant
- 1992–1995 NATO (North Atlantic Treaty Organization) Collaborative Research Grant
with Ukrainian organizations:
- Taras Shevchenko National University of Kyiv (Kyiv)
- Bogomoletz Institute of Physiology, NASU (Kyiv)
with foreign organizations:
- European Molecular Biology Laboratory (Grenoble, France)
- Institute Gustave-Roussy (Paris, France)
- Laboratory of Enzymology and Structural Biochemistry, CNRS (Gif-sur-Yvette, France)
- International Institute of Molecular and Cell Biology (Warsaw, Poland)
- Institute of Chemical Biology and Fundamental Medicine, SB RAS (Novosibirsk, Russia)
- Ilchenko, M.M., Rybak, M.Yu., Rayevsky, A.V., (...), Dubey, I.Ya., Tukalo, M.A. Substrate-assisted mechanism of catalytic hydrolysis of misaminoacylated tRNA required for protein synthesis fidelity. Biochemical Journal 476(4), pp. 719-732, 2019
- Volynets, G.P., Tukalo, M.A., Bdzhola, V.G., (...), Starosyla, S.A., Yarmoluk, S.M. Benzaldehyde thiosemicarbazone derivatives against replicating and nonreplicating Mycobacterium tuberculosis. Journal of Antibiotics 72(4), pp. 218-224, 2019
- Rybak, M.Y., Rayevsky, A.V., Gudzera, O.I., Tukalo, M.A. Stereospecificity control in aminoacyl-tRNA-synthetases: new evidence of d-amino acids activation and editing. Nucleic acids research. 47(18), pp. 9777-9788, 2019
- Volynets, G.P., Starosyla, S.A., Rybak, M.Y., (...), Yarmoluk, S.M., Tukalo, M.A. Dual-targeted hit identification using pharmacophore screening. Journal of Computer-Aided Molecular Design. 33(11), pp. 955-964, 2019
- M. Yu. Rybak, O. P. Kovalenko M.A., Tukalo. The Dual Role of the 2′-OH Group of A76 tRNA Tyr in the Prevention of D-tyrosine Mistranslation. J Mol Biol (2018) 430, 2670–2676
- A. V. Rayevsky, M. A. Tukalo. Computational approaches for parameterization of aminoacyl-tRNA synthetase substrates. Biopolymers and Cell. 2018. Vol. 34. N 3. P 239–247
- A.Rayevsky, M. Sharifi, M. Tukalo. A molecular dynamics simulation study of amino acid selectivity of LeuRS editing domain from Thermus thermophilus. Journal of Molecular Graphics and Modelling (2018) 84 P, 74-81 DOI:10.1016/j.jmgm.2018.06.015
- A.Rayevsky, M.Sharifi, M.Tukalo. Molecular modeling and molecular dynamics simulation study of archaeal leucyl-tRNA synthetase in complex with different mischarged tRNA in editing conformation. Journal of Molecular Graphics and Modelling DOI: http://dx.doi.org/doi:10.1016/j.jmgm.2017.06.022
- Boyarshin K.S., Priss A.E., Rayevskiy A.V., Ilchenko M.M., Dubey I.Ya., Kriklivyi I.A., Yaremchuk A.D., Tukalo M.A. A new mechanism of post-transfer editing by aminoacyl-tRNA synthetases: Catalysis of hydrolytic reaction by bacterial-type prolyl-tRNA synthetase. J. Biomol. Struct. Dynam. 2017. V. 35, N 3: 669-682
- Gudzera O. I., Golub A.G., Bdzhola V. G., Volynets G. P., Lukashov S.S., Kovalenko O. P., Kriklivyi I. A., Yaremchuk A.D., Starosyla S. A., Yarmoluk S. M., Tukalo M.A. Discovery of potent anti-tuberculosis agents targeting leucyl-tRNA synthetase. Bioorganic & Medicinal Chemistry. 2016, 24: 1023-131.
- Gudzera O. I., Golub A. G., Bdzhola V. G., Volynets G. P., Kovalenko O. P., Boyarshin K. S., Yaremchuk A.D., Protopopov M.V., Yarmoluk S. M., Tukalo M. A. Identification of Mycobacterium tuberculosis leucyl-tRNA synthetase (LeuRS) inhibitors among the derivatives of 5-phenylamino-2H-[1,2,4]triazin-3-one. Journal of Enzyme Inhibition and Medicinal Chemistry, DOI: 10.1080/14756366.2016.1190712.
- Boyarshin K., Priss A., Rayevskiy A, Ilchenko M, Dubey I, Kriklivyi I, Yaremchuk A. Tukalo M. A new mechanism of post-transfer editing by aminoacyl-tRNA synthetases: Catalysis of hydrolytic reaction by prolyl-tRNA synthetase of bacterial type. Journal of Biomolecular Structure and Dynamics. DOI: 10.1080/07391102.2016.1155171.
- Rayevsky A. V., Tukalo M. A. Molecular docking and molecular dynamics simulation studies on Thermus thermophilus leucyl-tRNA synthetase complexed with different amino acids and pre-transfer editing substrates. Biopolymers and Cell. 2016, 32(1):61–69.
- Rybak MYu, Kovalenko OP, Kriklivyi IA, Tukalo MA. Cloning, expression and purification of D-Tyr-tRNATyr –deacylase from Thermus thermophilus. Biopolymers & Cell, 2015;31(3):179–186.
- Boyarshin K, Priss A, Rayevskiy A, Ilchenko M, Dubey I, Kriklivyi I, Yaremchuk A, Tukalo M. A new mechanism of post-transfer editing by aminoacyl-tRNA synthetases: Catalysis of hydrolytic reaction by prolyl-tRNA synthetase of bacterial type. Journal of Biomolecular Structure & Dynamics. In Press.
- Gudzera OI, Golub AG, Bdzhola VG, Volynets GP, Lukashov SS, Kovalenko OP, Kriklivyi IA, Yaremchuk AD, Starosyla SA, Yarmoluk SM, Tukalo MA. Discovery of potent anti-tuberculosis agents targeting leucyl-tRNA synthetase. Bioorganic & Medicinal Chemistry. In Press.
- Kovalenko O, Gudzera O, Tukalo M. Mutagenesis probe into posttransfer editing mechanism of prokaryotic leucyl-tRNA synthetase. The FEBS Letters. In Press.
- Crepin T, Shalak VF, Yaremchuk AD, et al. Mammalian translation elongation factor eEF1A2: X-ray structure and new features of GDP/GTP exchange mechanism in higher eukaryotes. Nucleic Acids Research. 2014;1:1-10.
- Demianenko E, Ilchenko M, Grebenyuk A, et al. A theoretical study on ascorbic acid dissociation in water clusters. J. Mol. Model. 2014;20(3):1-8.
- Tukalo M. A., Yaremchuk G. D., Kovalenko O. P., Kriklivyi I. A., Gudzera O. I. Recognition of tRNAs with a long variable arm by aminoacyl- tRNA synthetases Biopolym. Cell. 2013; 29(4):311-323doi:10.7124/bc.000825
- Yaremchuk AD, Kovalenko OP, Gudzera OI, Tukalo MA. Molecular cloning, sequencing and expression in Escherichia coli cells Thermus thermophilus leucyl-tRNA synthetase Biopolym. Cell. 2011; 27(6): 436–41.doi: 10.7124/bc.000114
- Rock FL, Mao W, Yaremchuk A, et al. An antifungal agent inhibits an aminoacyl-tRNA synthetase by trapping tRNA in the editing site. Science. 2007;316(5832):1759–61. doi: 10.1126/science.1142189
- Tukalo M, Yaremchuk A, Fukunaga R, Yokoyama S, Cusack S. The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation. Nat Struct Mol Biol. 2005;12(10):923–30.doi:10.1038/nsmb986
- Lincecum TL Jr, Tukalo M, Yaremchuk A, et al. Structural and mechanistic basis of pre- and posttransfer editing by leucyl-tRNA synthetase. Mol Cell. 2003;11(4):951–63.doi:10.1016/S1097-2765(03)00098-4
- Yaremchuk A, Kriklivyi I, Tukalo M, Cusack S. Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition. EMBO J. 2002;21(14):3829–40.doi: 10.1093/emboj/cdf373
- Yaremchuk A, Cusack S, Tukalo M. Crystal structure of a eukaryote/ archaeon-like protyl-tRNA synthetase and its complex with tRNAPro(CGG). EMBO J. 2000; 19(17): 4745–58.doi:10.1093/emboj/19.17.4745
- Cusack S, Yaremchuk A, Tukalo M. The 2 A crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue. EMBO J. 2000;19(10):2351–61.doi:10.1093/emboj/19.10.2351
- Cusack S, Yaremchuk A, Tukalo M. The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site. EMBO J. 1996; 15(11):2834–42.
- Biou V, Yaremchuk A, Tukalo M, Cusack S. The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Science. 1994;263(5152):1404–10.doi:10.1126/science.8128220
- Belrhali H, Yaremchuk A, Tukalo M, et al. Crystal structures at2.5 angstrom resolution of seryl-tRNA synthetase complexedwith two analogs of seryl adenylate. Science. 1994; 263(5152):1432–6.doi:10.1126/science.8128224