Fig. 4: Analysis of individual parameters for PUM2 and PUF4 predictive thermodynamic models. | Nature Communications

Fig. 4: Analysis of individual parameters for PUM2 and PUF4 predictive thermodynamic models.

From: A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4

Fig. 4

a PUF4 and PUM2 additive model parameters, optimized for each RBP (from Table 1). b Scatterplot of all bound terms (ΔΔGbX) from the PUM2 and PUF4 predictive models. The dashed line corresponds to x = y (R2 = 0.86; RMSE = 0.5 kcal/mol). c Flipping parameters (ΔΔGfY) for PUF4 and PUM2 optimized with the data for each. NN indicates any two bases flipped at the given position (see also Table 1). d Scatterplot of base flip terms (ΔΔGfY) in the PUM2 and PUF4 predictive models. Open symbols are for flips at position 6/7 (single flips denoted by squares and double flips denoted by triangles) and closed are for flips at the 3/4, 4/5, or 5/6 positions (see Fig. 3a for nomenclature). Limits are shown with arrows in the figure and values are from Table 1 and ref. 34.

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