Fig. 3

Adaptive substitutions alter RNA recognition domain (RD) structure and RNA-binding preference throughout RIG-like receptor (RLR) evolution. We inferred structural models of human and ancestral RLR RDs (see Figs. 1 and 2) bound to blunt-ended double-stranded RNA and dsRNA having a 5′ triphosphate (5ppp). We show the central structures of each RD-RNA from replicate molecular dynamics simulations, with electrostatic potential (kT/e) displayed on the molecular surface (see Methods). Dotted ovals indicate the location of the canonical RNA binding loop on each structural model. We resurrected ancestral RLR RDs and measured steady-state (Kd) and initial (Km) RNA binding affinities (see Methods). We plot –log-transformed binding affinities, with longer bars indicating higher affinity. Standard errors over three replicates are indicated. For ancRLR, ancMDA5/LGP2a and ancMDA5/LGP2b, we compare RNA binding affinities measured for the RD to affinities measured using the combined helicase + pincer + RD domains