A theoretical study on ascorbic acid dissociation in water clusters. Recognition of tRNAs with a long variable arm by aminoacyl- trna synthetases biopolym. 2013; 29(4 311-323 doi:10.7124/bc.000825 Yaremchuk ad, kovalenko op, gudzera oi, tukalo. Molecular cloning, sequencing and expression in Escherichia coli cells Thermus thermophilus leucyl-trna paperless synthetase biopolym. Doi:.7124/bc.000114 Rock fl, mao w, yaremchuk a,. An antifungal agent inhibits an aminoacyl-trna synthetase by trapping trna in the editing site. Doi:.1126/science.1142189 tukalo m, yaremchuk a, fukunaga r, yokoyama s, cusack. The crystal structure of leucyl-trna synthetase complexed with trnaleu in the post-transfer-editing conformation.
Journal of biomolecular Structure dynamics. Gudzera oi, golub ag, bdzhola vg, volynets gp, lukashov ss, kovalenko op, kriklivyi ia, yaremchuk ad, starosyla sa, yarmoluk sm, tukalo. Kovalenko o, gudzera o, tukalo. Mutagenesis probe into posttransfer editing mechanism of prokaryotic leucyl-trna synthetase. Crepin small t, shalak vf, yaremchuk ad,. Mammalian translation elongation factor eef1A2: X-ray structure and new features of gdp/gtp exchange mechanism in higher eukaryotes. Demianenko e, ilchenko m, grebenyuk a,.
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. Molecular docking and molecular dynamics simulation studies on Thermus thermophilus leucyl-trna synthetase complexed with different amino acids and pre-transfer editing substrates. Rybak myu, kovalenko op, kriklivyi ia, tukalo. Cloning, expression and purification of d-tyr-trnatyr deacylase from Thermus thermophilus. Biopolymers cell, 2015;31(3 179186. Boyarshin k, priss a, rayevskiy a, ilchenko m, dubey i, kriklivyi i, yaremchuk a, tukalo.
The paul Berg Papers: Protein, synthesis, tumor
The contract pr 059/514.11. Shevchenko (scientific supervisor. International Grants: gdri (International Research Networks) Project: From molecular to cellular events in human pathologies (scientific supervisors Prof. Lavrik ) th Framework Programme (FP7) FP7- inco-2011-6, era-wide project: Strengthening cooperation in Molecular biomedicine between eu and ukraine, combiom (scientific supervisor Prof. Elskaya) stcu (Science and Technology center in Ukraine) Research Grants stcu research Grants nato (North Atlantic Treaty Organization) Collaborative research Grant Collaboration: with Ukrainian organizations: Taras Shevchenko national University of kyiv (kyiv) Bogomoletz Institute of Physiology, nasu (kyiv) with foreign organizations: European Molecular biology laboratory.
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:.2017.06.022 boyarshin. A new mechanism of post-transfer editing by aminoacyl-trna net synthetases: Catalysis of hydrolytic reaction by bacterial-type prolyl-trna synthetase. 35, n 3: 669-682 Gudzera. Discovery of potent anti-tuberculosis agents targeting leucyl-trna synthetase. Identification of Mycobacterium tuberculosis leucyl-trna synthetase (leurs) inhibitors among the derivatives of journal of Enzyme Inhibition and Medicinal Chemistry, doi:.1080/14756366.2016.1190712. Boyarshin., Priss., rayevskiy a, ilchenko m, dubey i, kriklivyi i, yaremchuk.
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. 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.
Trna-assisted mechanism of post-transfer editing by leucyltrna synthetase 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. Exploitation of structural differences of human and pathogenic bacterial prolyl-trna synthetases for the identification of novel inhibitors as potential anti-pathogen drugs National Grants: Projects of National Academy of Sciences of Ukraine: Progect: Target-directed search for a new antibacterial, antiviral and antitumor agents (scientific supervisor. Tukalo) 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. 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.
Nutrition metabolism Abstract The application
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. Cloverleaf structures. Thermophilus trnatyr, trnaser and trnaleu with position of phosphates protected by cognate synthetase from alkylation with ethylnitrosourea fig. Recognition of tRNAs with a long variable arm by cognate aminoacyl-trna synthetases 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 interests trna in an extra editing domain.
of Hisrstt (the left) or tyrosyl-adenylate analogue binds in the active site of Tyrrstt (the right). 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 1120 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. 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.
The research of the last years was directed at the identification of the structural review 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. 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.
Somerset Academy - central Miramar Campus
member of National Academy of Sciences of Ukraine, deputy director for scientific recearch Tel: (380-44). Fax (380-44) il: Group of Molecular Pharmacology, head: Zenoviy. Group of systems biology, head: Group of systems biology, professor,. Education and Degrees: Graduate Student, taras Shevchenko national University of kyiv, kyiv, ukraine. (molecular biology) 1989. (molecular biology) 2005 Professor, taras Shevchenko national University of kyiv 2009 Corresponding Member of nasu 2018 Member of National Academy of Sciences of Ukraine. Professional Employment: 1973 Research Assistant, Institute of Molecular biology and Genetics (imbg nasu, kyiv, ukraine (molecular biology) Visiting Scientist at the wallpaper novosibirsk Institute of bioorganic Chemistry, novosibirsk, russia junior Research Scientist, Group leader, imbg nasu, kyiv, ukraine senior Research Scientist, Group leader, imbg nasu, kyiv. 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 Howard Hughes Medical Institute International Research Grant. Research Area: Study on the molecular basis of decoding genetic information, translation quality control and rna-protein recognition.