Computational modeling and molecular dynamics simulations of mammalian cytoplasmic tyrosyl-tRNA synthetase and its complexes with substrates.
Cytoplasmic tyrosyl-tRNA synthetase (TyrRS) is one of the key enzymes of protein biosynthesis. TyrRSs of pathogenic organisms have gained attention as potential targets for drug development. Identifying structural differences between various TyrRSs will facilitate the development of specific inhibitors for the TyrRSs of pathogenic organisms. However, there is a deficiency in structural data for mammalian cytoplasmic TyrRS in complexes with substrates. In this work, we constructed spatial structure of full-length Bos taurus TyrRS (BtTyrRS) and its complexes with substrates using the set of computational modeling techniques. Special attention was paid to BtTyrRS complexes with substrates [L-tyrosine, K+and ATP:Mg2+] and intermediate products [tyrosyl-adenylate (Tyr-AMP), K+and PPi:Mg2+] with the different catalytic loop conformations. In order to analyze their dynamical properties, we performed 100 ns of molecular dynamics (MD) simulations. MD simulations revealed new structural data concerning the tyrosine activation reaction in mammalian TyrRS. Formation of strong interaction between Lys154 and γ-phosphate suggests the additional role of CP1 insertion as an important factor for ATP binding. The presence of a potassium-binding pocket within the active site of mammalian TyrRS compensates the absence of the second lysine in the KMSKS motif. Our data provide new details concerning a role of K+ions at different stages of the first step of the tyrosylation reaction, including the coordination of substrates and involvement in the PPireleasing. The results of this work suggest that differences between ATP-binding sites of mammalian and bacterial TyrRSs are meaningful and could be exploited in the drug design.
a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.|b Department of Biotechnology , National Aviation University , 1, Kosmonavta Komarova Str., Kyiv , 03058 , Ukraine.
Vladyslav O
http://orcid.org/0000-0001-9523-9089
VO
Kravchuk
a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.
Oleksandr V
http://orcid.org/0000-0002-8150-4416
OV
Savytskyi
a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.
Konstantin O
KO
Odynets
a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.|c Institute of High Technologies , Taras Shevchenko National University of Kyiv , 64, Volodymyrs'ka Str., Kyiv , 01601 , Ukraine.
Vasyl V
http://orcid.org/0000-0002-2522-9907
VV
Mykuliak
a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.|c Institute of High Technologies , Taras Shevchenko National University of Kyiv , 64, Volodymyrs'ka Str., Kyiv , 01601 , Ukraine.
Alexander I
AI
Kornelyuk
D000249:Adenosine Monophosphate / Q000031:analogs & derivatives / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D000818:Animals; D020134:Catalytic Domain / Q000502:physiology; D002417:Cattle; D003198:Computer Simulation; D003593:Cytoplasm / Q000378:metabolism*; D008322:Mammals / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D013379:Substrate Specificity; D014443:Tyrosine / Q000031:analogs & derivatives / Q000378:metabolism*; D014448:Tyrosine-tRNA Ligase / Q000378:metabolism*
D000249:Adenosine Monophosphate; D014443:Tyrosine; C019586:tyrosinyl-5'-AMP; D000255:Adenosine Triphosphate; D014448:Tyrosine-tRNA Ligase
ATP; KMSKS; MolDynGrid; aminoacyl-tRNA synthetase; docking; molecular modeling and dynamics