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

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-a-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.

Flexible 3D structure of Bos taurus tyrosyl-tRNA synthetase suggests the existence of hinge mechanism provided by conservative Gly353 at interdomain linker

“…Recently, we have performed an analysis of the YCD2 fragment of this model, comprised of the a-helical part of N-domain, the linker and the C-domain. The results reported in [34], revealed a specific behavior of the linker in ten-nanosecond time-frame. It changes conformation from extended and disordered to more compact one with short transient a-helical structures, supporting the currently proposed general model of the interdomain linker role in modulation of the enzyme activity [35].…”