Fig. 5
From: Modification of messenger RNA by 2′-O-methylation regulates gene expression in vivo
Molecular dynamics modeling of Pxdn Nm codon modification at the ribosomal A-site. SnoRNA-guided Nm modification on Pxdn mRNA is predicted at the first position of an AAG lysine codon. Our model of the ribosomal A-site included the mRNA, tRNA, and rRNA, but only the first two nucleotides of the AAG codon (A1 and A2) and the relevant monitoring rRNA nucleotides (A1492 and A1493) are shown for clarity. Hydrogen bonds are shown as yellow lines. Movies of the full trajectories are available online. a, b Representative configurations of the canonical interaction. For the A1:A1493 interaction, note that A1 can serve as the hydrogen bond donor (a) or acceptor (b). c, d Representative configurations of the Am1 and Am2 modifications, respectively, where the van der Waals radius for the Nm methyl group is shown as a yellow-green sphere. e–j The A1:A1493 and A2:A1492 donor-acceptor distances are shown for 500 ns simulations. Distances < 0.32 nm are consistent with hydrogen bonding interactions, and the percent of time that each interaction falls within this range are also shown. e, f canonical (unmodified). g, h Am1 (Am at first codon position). i, j Am2 (Am at second codon position)
