Figure 4
From: Modulation of thermal noise and spectral sensitivity in Lake Baikal cottoid fish rhodopsins
Spectral tuning sites in Baikal cottoid rhodopsins.
(a) Direct (side-chain replacement) and indirect (conserved residue or water molecule reorientation) mechanisms for color-tuning based on Nakanishi point charge model. The effect of each mechanism on the ΔE variation (e.g. S1 destabilization or S0 stabilization) is illustrated by the corresponding bar diagrams. Top. Geometrical variations associated with the Y261F and G114A substitutions characterizing the transition from P. kneri (red) and A. korotneffi (blue). Bottom. Water molecule (WAT2) reorientation caused by the A292S substitution characterizing the same transition. (b) Spectral-tuning mechanism related to the Y261F substitution between P. kneri (red) and P. jettelesi (yellow). (c) Spectral-tuning mechanism related to the A292S and G114A substitutions between P. jettelesi and A. korotneffi (blue). (d) Cavity and extra-cavity substitutions associated with the transitions between different rhodopsins. The full arrows indicate the proposed evolutionary relationship between the corresponding species when assuming P. jettelesi to be the closest to the ancestor. In contrast, the grey arrow indicates the substitutions involved in the transition between littoral and abyssal species.
