Role of the transfer ribonucleic acid (tRNA) bound magnesium ions in the charging step of aminoacylation reaction in the glutamyl tRNA synthetase and the seryl tRNA synthetase bound with cognate tRNA

Abstract

Aminoacylation reaction is the first step of protein biosynthesis. Transfer RNA (tRNA) is charged with an amino acid in this reaction and the reaction is catalyzed by aminoacyl tRNA synthetase enzyme (aaRS). In the present work, we use classical molecular dynamics simulation to show that the tRNA bound Mg²⁺ ions significantly influence the charging step of class I ^TtGluRS: Glu-AMP: tRNA^Glu and class II dimeric ^TtSerRS: Ser-AMP: tRNA^Ser. The CCA end of the acceptor terminal is disordered in the absence of coordinated Mg²⁺ ions and the CCA end can freely explore beyond the specific conformational space of the tRNA in its precharging state. A balance between the conformational disorder of the tRNA and the restriction imposed on the CCA terminal via coordination with the Mg²⁺ ions is needed for the placement of the CCA terminal in a precharging state organization. This result provides a molecular-level explanation of the experimental observation that the presence of Mg²⁺ ions is a necessary condition for a successful aminoacylation reaction.

Communicated by Ramaswamy H. Sarma

Keywords:

• Aminoacylation
• magnesium ion
• transfer RNA
• molecular dynamics simulation
• metadynamics

Acknowledgments

A.S thanks to DST INSPIRE Fellowship. This work is supported by a DST SERB grant to N.N. Partial support by grants from the UGC SAP DRS II program and the University of Kalyani is acknowledged. We thank anonymous reviewers of the manuscript for suggestions that helped to improve the manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work is supported by a SERB project grant (to N.N.) from DST, India.