Conformational flexibility of interdomain linker in bovine tyrosyl-tRNA synthetase studied by molecular dynamics simulation

Pydiura, N. A.; Tereshchenko, F. A.; Kornelyuk, A. I.

doi:10.7124/bc.000749

Biopolym. Cell. 2006; 22(6):433-438.

http://dx.doi.org/10.7124/bc.000749

Structure and Function of Biopolymers

Conformational flexibility of interdomain linker in bovine tyrosyl-tRNA synthetase studied by molecular dynamics simulation

1Pydiura N. A., 1Tereshchenko F. A., 1Kornelyuk A. I.

Institute of Molecular Biology and Genetics, NAS of Ukraine
150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

Here we report a study of molecular dynamics of a YCD2 fragment of mammalian tyrosyl-tRNA synthethase (Asp322-Ser528), which includes the COOH-terminal cytokine-like domain, intermodular flexible linker, and H5-α-helix of catalytic core of synthetase. Our calculations show that while compact C-terminal domain was less flexible and relatively stable, the interdomain linker shows a high degree of conformational changes. After short relaxation time it forms a short helix-like structure, which may be involved in the regulation of domain interaction and modulation of protein activities.

Keywords: Tyrosyl-tRNA synthetase, cytokine, C-module, molecular dynamics, linker flexibility

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