On the Bioactive Conformation of the Rhodopsin Chromophore: Absolute Sense of Twist around the 6-s-cis Bond

Abstract

Incubation of opsin with synthetic 6-s-locked retinoids 2a and 2b only led to pigment formation from the alpha-locked 2a, the CD spectrum of which was similar to that of native rhodopsin (Rh). This establishes that the 6-s-bond of the chromophore in rhodopsin is cis, and that its helicity is negative. Earlier cross-linking studies showed that the 11-cis to all-trans photoisomerization occurring in the batho-Rh to lumi-Rh conversion induces a flip over of the side carrying the ring moiety. The GTP-binding assay of pigment Rh-(2a), incorporating retinal analogue 2a, has shown that its activity is 80% that of the native pigment. That is, the overall conformation around the 6-s bond is retained in the steps leading to G-protein activation.

Dynamic Structure of Retinylidene Ligand of Rhodopsin Probed by Molecular Simulations

“…By contrast, the retinal conformation becomes more restricted upon binding to rhodopsin, where it functions as an inverse agonist. It is interesting that in both bacteriorhodopsin 51,53 and sensory rhodopsin, 54 retinal is 6-s-trans; while in dark-adapted rhodopsin it is widely thought to adopt the 6-s-cis conformation 33,40,55 .…”

“…The torsion about the C6-C7 bond defines the orientation of the β-ionone ring relative to the polyene chain. Free retinal has been shown with both experimental 51 and computational 39 methods to exist as multiple isomers represented by 6-s-cis and 6-s-trans states, which is consistent with CD data 40,41,52 . By contrast, the retinal conformation becomes more restricted upon binding to rhodopsin, where it functions as an inverse agonist.…”

“…We were able to interpret experimental results, including hydrogen-out-of-plane (HOOP) wagging modes from Raman vibrational spectroscopy 17 and solid state 2 H NMR spectra 33 , cf. Comparison was made to detailed experimental data in all cases 17,33,40,41 .…”

“…Gas phase computations indicate equal probability for the two 6-s-cis conformers, suggesting that the asymmetry in the distribution for the β-ionone ring of retinal when bound to rhodopsin is most likely due to interactions with the surrounding protein side chains. Previous experiments using chemically modified ligands have demonstrated that the binding cavity differentiates between retinal enantiomers 16,40 . Our MD simulations imply that the cavity has a moderate selectivity for the negatively twisted enantiomer, yielding positive ellipticity in circular dichroism (CD) spectra consistent with experimental data 40 .…”

Possible role of the 11- cis -retinyl conformation in controlling the dual decay processes of excited rhodopsin

“…In solution the 6-s-cis form is likely to undergo rapid equilibration with the higher energy 6-s-trans form (10,11). However, when fitted into the hydrophobic pocket of opsin, evidence suggests that the retinyl chromophore exists exclusively in the 6-s-cis form (12). [Interestingly, for the corresponding hydrophobic pocket in bacterioopsin, the ring-chain conformation of the all-trans-retinyl chromophore is exclusively 6-s-trans (13).]…”