Fig. 2.
The dependence of the energy of charge–charge interactions on the number of amino acid substitutions (or the percentage of substitutions relative to the total number of amino acid residues) in AcPh (A) and Cdc42 (C). Each small dot corresponds to a different sequence. The sequences selected for experimental verification are shown in large symbols: AcPh-wt or Cdc42-wt, black circles; AcPh-des, red squares; Cdc42-des1, blue squares; and Cdc42-des2, red triangles. (B and D) The corresponding per residue energies of charge–charge interactions as calculated by TKSA model are given in B (AcPh-wt, black bars; AcPh-des, red bars) and D (Cdc42-wt, black bars; Cdc42-des1, red bars; Cdc42-des2, blue bars). Positive energies represent overall unfavorable interactions of a given residue with all other ionizable residues in the proteins, whereas negative values of ΔGqq reflect overall favorable interactions.