Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study - Fig 4

(A) Bird’s-eye view of the Rbfox•pre-miR20b complex. (B)-(H) Close-up views of the interactions observed at the binding interface during MD simulations. The H-bonds are indicated by dotted red lines. The depicted snapshots belong to the representative structures of the 20 clusters (“MD-adapted structure ensemble”), which have the highest agreement with NMR NOE data. (I) Scheme of the interactions. Circle and arrowheads depict interaction with RNA bases or phosphate groups, respectively.