Figure 2

λ_max and E_a^T values of Baikal cottoid fish rhodopsins.

(a) Experimental (blue diamonds) and computed (purple circles) λ_max of the selected rhodopsins (the computed values are scaled by applying a factor of 1.03 and 1.05 to the corresponding ΔE of the A1 and A2 models respectively). The straight line indicates the linear relationship of 18 identical-opsin pairs selected by Dartnall and Lythgoe. The ΔE values for the isolated chromophores of the computed set are also displayed (black triangles). (b) Superimposed S₀ equilibrium geometries of A1 retinal chromophores in C. inermis (green), P. jettelesi (orange), A. korotneffi (blue) and P. kneri (red). The relevant bond lengths and backbone dihedral angle are given in Å and degrees respectively. (c) Balloon diagram displaying the difference between the S₁ and S₀ charge (S₁/S₀ charge difference, in electron units) distributions at the S₀ equilibrium structure of P. jettelesi. (d) Computed thermal isomerization E_a^T (with a scaling factor of 1.18 applying to the A1 models, see SI for details) plotted as a function of the inverse of the corresponding λ_max for pigments with the A1 chromophores in the protein (black circles), isolated (gray triangles) and in the protein with no point charges (red squares). Straight lines indicate the ideal linear relationship. The significant difference between the computed 35–40 kcal mol⁻¹ E_a^T value (this work) and the ca. 22 kcal mol⁻¹ value measured in the 288–298 K range assuming an Arrhenius kinetics has been discussed in ref. An updated discussion is given in the SI Appendix Section 6. (e) Transitions state geometries of the A1 retinal chromophore in A. korotneffi (blue) and P. kneri (red) rhodopsins. The relevant bond lengths and backbone dihedral angle are given in Å and degrees respectively. (f) Difference between the charge distributions between the S₀ transition state structure and equilibrium structure for P. jettelesi (TS/S₀ charge difference).