Origin of a Double-Band Feature in the Ethylenic C═C Stretching Modes of the Retinal Chromophore in Heliorhodopsins

Abstract

Photoreceptor proteins play a critical role in light utilization for energy conversion and environmental sensing. Rhodopsin is a prototypical photoreceptor protein containing a retinal group that functions as a light-receptive site. It is essential to characterize the structure of the retinal chromophore because the chromophore structure, along with retinal–protein interactions, regulates which wavelengths of light are absorbed. Resonance Raman spectroscopy is a powerful tool to characterize chromophore structures in proteins. The resonance Raman spectra of heliorhodopsins, a recently discovered rhodopsin family, were previously reported to exhibit two intense ethylenic CC stretching bands never observed for type-1 rhodopsins. Here, we show that the double-band feature in the ethylenic CC stretching modes is not due to structural inhomogeneity but rather to the retinal polyene chain’s linear structure. It contrasts with bent all-trans chromophore in type-1 rhodopsins. The linear structure of the chromophore results from weak atomic contacts between the 13-methyl group and a nearby Trp side chain, which can slow thermal reisomerization in the photocycle. It is possible that the deceleration of reisomerization increases the lifetime of the signaling intermediate for photosensory function.

A Proteorhodopsin-Related Photosensor Expands the Repertoire of Structural Motifs Employed by Sensory Rhodopsins

“…The secondary higher-frequency peak is strongly D 2 O-dependent (presumably being coupled to NH vibrations), shifting to 1527 cm –1 . This behavior is reminiscent of recently observed Raman spectra of heliorhodopsins, where it was interpreted as originating from a linear rather than bent retinal polyene chain, but the ethylenic stretch band split is even more pronounced in Proteo-SRs. Second, there is a prominent unusual D 2 O-dependent HOOP (hydrogen out-of-plane) band at 980 cm –1 , with a number of smaller D 2 O-independent bands at 959, 880, and 833 cm –1 , which suggest strongly twisted retinal skeleton, especially in the vicinity of the retinal Schiff base .…”

Cis–Trans Reisomerization Preceding Reprotonation of the Retinal Chromophore Is Common to the Schizorhodopsin Family: A Simple and Rational Mechanism for Inward Proton Pumping

“…40 The positions of the Trp and Tyr residues that sandwich the C 13 �C 14 region of the chromophore affect the linearity of the polyene chain in heliorhodopsins. 41 These results strongly suggest that the amino acid side chains in opsin are in close contact with the polyene chain and can thus affect the rate of cis−trans thermal isomerization. Figure 6 compares the relative positions of the side chains of the residues for SzR4, HsBR, and HeR from the Thermoplasmatales archaeon (TaHeR).…”

“…We previously discussed the importance of tight atomic contacts between the retinal chromophore and nearby residues in microbial rhodopsins. , High atomic packing is generally crucial for successive structural changes to propagate to spatially distinct sites . The contacts between the methyl groups of the chromophore and the side chain of a Trp residue (W222) drive protein motion essential to proton transport in Gloeobacter rhodopsin (GR) .…”

“…The contacts between the methyl groups of the chromophore and the side chain of a Trp residue (W222) drive protein motion essential to proton transport in Gloeobacter rhodopsin (GR) . The positions of the Trp and Tyr residues that sandwich the C 13 C 14 region of the chromophore affect the linearity of the polyene chain in heliorhodopsins . These results strongly suggest that the amino acid side chains in opsin are in close contact with the polyene chain and can thus affect the rate of cis – trans thermal isomerization.…”

“…These differences in the positions of the side chains result in the polyene chain being linear in HeRs. 41 In SzR4, the side chain of the Trp residue in contact with the methyl group (W154) is shifted toward the Schiff base compared with that of HsBR, resulting in tighter contact between the Trp side chain and the methyl group. Indeed, the distances between the carbon atom of the methyl group and the center of mass for the indole-ring atoms of the Trp residue were 3.50 and 3.97 Å for SzR4 7 and HsBR, 43 respectively.…”