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: tRNAGlu and class II dimeric TtSerRS: Ser-AMP: tRNASer. 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
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.