Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with λ-dynamics

Example λ-dynamics predictions of how RNA modifications may affect binding to human Pumilio 1. The original RNA base is reported, along with the base change (*, RNA name and chemical structure above) and noted relative free energy binding change measured (ΔΔG_bind, kcal/mol, 50 nsec simulations) with CHARMM36 and Amber force fields. Predicted decrease in binding affinity, positive ΔΔG_bind, in red. Predicted increase in binding affinity, negative ΔΔG_bind, in green. Results highlight modifications tested in vitro. Sites refer to RNA positions described in Figure 1. See Supplemental Table S2 for complete screening results.