Structure-Based Simulations for Folding of a tRNA Isodecoder

The N2,N2-dimethylguanosine (m2,2G) modification at the G27 nucleotide of transfer RNA (tRNA) is a crucial modification known to impact tRNA folding. Although some functional implications of m2,2G have been characterized, little is known about the molecular details of the effect of this modification on tRNA folding. In this work, we study folding of a tRNA isodecoder molecule by conducting all-atom structure-based simulations initiated from an ensemble of unfolded configurations. We observed that the folding of the modified tRNA proceeds cooperatively and hierarchically, beginning with the folding of the anticodon stem loop, followed by the folding of the D-stem loop or T-stem loop, and ending with the folding of the acceptor stem, thereby resulting in a fully folded configuration. However, the folding of the unmodified tRNA isodecoder revealed partially-folded intermediate configurations to be more favorable than a fully folded state. These results provide insights into the role of methylation in the folding of the tRNA isodecoder studied here and have broader implications for the folding of other tRNA species.