Biopolymers and cell. 2006; 22 (6): 433 - 438

Conformational Flexibility of Interdomain Linker in Bovine Tyrosyl-tRNA Synthetase Studied by Molecular Dynamics Simulation

N. Pydiura, F. Tereshchenko, A. Kornelyuk

In this paper 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 (17 amino acids), 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 two short α-helix-like structures, which may be involved in the regulation of domain interaction and modulation of protein activities.

Key words: Tyrosyl-tRNA synthetase, cytokine, C-module, molecular dynamics, linker flexibility.