Figure 3

Effects of point charges of specific cavity residues between the two extreme cases: P. kneri and A. korotneffi.

Apolar and polar residues are reported in gray and cyan, respectively and Gly residue (hydrogen) is shown as small gray sphere. The chromophore and the E113 counterion are shown in tube representation. The labels indicate residues that are not conserved in at least one of the four pigments of the cottoid fish set. (a) Retinal-binding pockets of the pigments with the A2 chromophore. ΔE-ΔE_off >0.5 kcal mol⁻¹ in absolute value are labelled in red (negative shift) and blue (positive shift). The corresponding values are given in parenthesis in kcal mol⁻¹ and represented by balloons. (b) Retinal-binding pockets of transition state with the A1 chromophores viewed with substitution (reported in yellow) at residue 261. E_a^T-E_a^T_off >0.5 kcal mol⁻¹ in absolute value are labelled in red (negative shift) and blue (positive shift) and given in parenthesis in kcal mol⁻¹. The dashed lines indicate hydrogen bonds. (c) The same data for the substitution of residue 292.