Extended Data Fig. 4: MD simulation-based prediction supports the ΨGA preference of the screened mmtRNAPyl(UCA)-A37G variant. | Nature

Extended Data Fig. 4: MD simulation-based prediction supports the ΨGA preference of the screened mmtRNAPyl(UCA)-A37G variant.

From: RNA codon expansion via programmable pseudouridine editing and decoding

Extended Data Fig. 4: MD simulation-based prediction supports the ΨGA preference of the screened mmtRNAPyl(UCA)-A37G variant.

a-c, Structural comparison among the ribosome-tRNA-mRNA complex from cryo-EM (PDB ID: 4JYA) (a), and all-atom MD simulation (b), along with the merged complex structures between cryo-EM and MD (c). The results show that the tRNA and mRNA align well between the structures from cryo-EM and MD simulation. d, The paired probability of the averaged trajectories demonstrating the binding between tRNA variants and UGA- or ΨGA-containing mRNAs. e-h, Centroids of the tRNA-mRNA paring structures of the wild-type mmtRNAPyl(UCA) (e,f) and the selected mmtRNAPyl(UCA)-A37G (g,h), illustrating that mmtRNAPyl(UCA)-37G forms more stable hydrogen bonds to ΨGA codon than to UGA codon.

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