Fig. 4: MD simulations and FMO calculations elucidated the energetic impact of RNA sequences on the association with DMDA-PatA. | Nature Communications

Fig. 4: MD simulations and FMO calculations elucidated the energetic impact of RNA sequences on the association with DMDA-PatA.

From: DMDA-PatA mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs

Fig. 4

a Overlaid simulated structures (n = 10) of polypurine RNA•DMDA-PatA•eIF4A1 complexes analyzed by MD simulation. The complexes with RNAs possessing the indicated substitutions were investigated. b The interaction energy between DMDA-PatA and the indicated bases along the investigated complexes through FMO calculations. The data are presented as the mean (bar) for 10 simulated complexes (point). c The difference in the interaction energy between DMDA-PatA and the indicated bases from the original sequence (6GAGA9). See b for the source data. The color scale is shown. d The difference in the electrostatic interaction energy between DMDA-PatA and the indicated bases from the original sequence (6GAGA9). See Supplementary Fig. 4c for the source data. The color scale is shown. e, f Representative structures obtained by MD simulations (at 100 ns) with 6GAGA9 (original sequence) or 6AGAG9. The net charge (e) on the indicated groups and the distances are shown (mean ± s.d. for 10 simulated structures). Source data are provided as a Source Data file.

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