Mechanism of Ribosomal A1493 in Stabilizing and Rigidly Supporting the Codon-Anticodon Helix During tRNA Recognition

The ribosome ensures translational accuracy by monitoring codon-anticodon interactions at the A site decoding center, yet the mechanism of conserved nucleotides contributing to this process remains controversial. Here, we performed molecular dynamics simulations based on a tRNA recognition intermediate that reflects the ribosomal state during ongoing tRNA recognition. We systematically investigated the coupling between the stability of the first codon-anticodon base pair and the conformational dynamics of A1493 in both cognate and near-cognate tRNA systems. Our results show that A1493 stabilizes the codon-anticodon helix through an entropic mechanism and functions as a "wedge" to provide rigid support for it. The correct flipping of A1493 is facilitated by van der Waals interactions with the residue at position 37 of tRNA, highlighting the crucial role of steric complementarity in the decoding center. However, the flipping of A1493 lacks specificity for different tRNAs due to conformational changes of A1913, suggesting that the large ribosomal subunit may also participate in tRNA recognition. We also explored changes in codon-anticodon stability during translocation. Together, these findings refine the mechanism by which conserved ribosomal nucleotides participate in decoding.