Molecular dynamics simulations of cognate and non-cognate AspRS-tRNA^Asp complexes

Abstract

Aspartyl tRNA synthetase (AspRS), one of the 20 aminoacyl-tRNA synthetases, plays an important role in protein synthesis by catalyzing the aminoacylation reaction and synthesises Aspartyl-tRNA (tRNA^Asp). A typical three-dimensional structure of AspRS comprises three distinct domains for the recognition of cognate tRNA and catalysis, namely, anti-codon binding domain/N-terminal domain, hinge domain and catalytic domain through their interactions with anti-codon loop, D-stem and acceptor arm of cognate tRNA, respectively. In this work, we have studied the structural characteristics of each domain of AspRS to understand the recognition mechanism of tRNA^Asp using molecular dynamics simulations. The dynamics of AspRS-tRNA^Asp complexes from E.coli (cognate and non-cognate), S.cerevisiae (cognate) and T.thermophilus (non-cognate) were compared to understand the differences in recognition of cognate and non-cognate tRNAs. Our results explain that the conformational changes associated with the recognition of tRNA occur only in the cognate complexes. Among the cognate complexes, the conformational changes in yeast AspRS are highly controlled during tRNA^Asp recognition than that of in the E. coli AspRS. Moreover, the functional motions required for the tRNA recognition are observed only in the cognate complexes, and the conformational changes in AspRS and their recognition of tRNA^Asp are organism specific.

Communicated by Ramaswamy H. Sarma

Keywords:

• Aspartyl tRNA synthetase
• tRNA recognition
• cognate and non-cognate tRNAs
• AspRS
• aspartyl-tRNA
• protein-RNA complex
• MD simulation

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

We thank Bioinformatics Facility, High Performance Computing Facility and Indian Institute of Technology Madras for computational facilities. This research was partially supported by Department of Science and Technology, Government of India.