Unique Retinal Binding Pocket of Primate Blue-Sensitive Visual Pigment

Nonaka, Yoichi; Hanai, Shunpei; Katayama, Kota; Imai, Hiroo; Kandori, Hideki

doi:10.1021/acs.biochem.0c00394

Cited by 4 publications

(2 citation statements)

References 52 publications

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“…Photoequilibria of SpiRh1 with the Bathointermediate and Isoproduct at 77 K. Visual pigments exhibit photoequilibria among 11-cis (resting state; SpiRh1 or R in this paper), all-trans (bathointermediate; Batho or B), and 9-cis (isoproduct; Iso or I) forms at 77 K, although the 9-cis form does not appear for the Monkey Blue-sensitive pigment. 55 We first examined isomeric forms produced in SpiRh1 at 77 K. SpiRh1 was expressed in COS-1 cells, followed by the addition of 11-cis retinal, solubilized in DDM, and purified by 1D4column, whose absorption spectrum is shown in Figure S1. Absorption maximum at 533 nm confirms the 11-cis chromophore in the SpiRh1 sample.…”

Section: ■ Resultsmentioning

confidence: 99%

Difference FTIR Spectroscopy of Jumping Spider Rhodopsin-1 at 77 K

et al. 2023

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Animal visual rhodopsins can be classified into monostable and bistable rhodopsins, which are typically found in vertebrates and invertebrates, respectively. The former example is bovine rhodopsin (BovRh), whose structures and functions have been extensively studied. On the other hand, those of bistable rhodopsins are less known, despite their importance in optogenetics. Here, low-temperature Fourier-transform infrared (FTIR) spectroscopy was applied to jumping spider rhodopsin-1 (SpiRh1) at 77 K, and the obtained light-induced spectral changes were compared with those of squid rhodopsin (SquRh) and BovRh. Although chromophore distortion of the resting state monitored by HOOP vibrations is not distinctive between invertebrate and vertebrate rhodopsins, distortion of the all-trans chromophore after photoisomerization is unique for BovRh, and the distortion was localized at the center of the chromophore in SpiRh1 and SquRh. Highly conserved aspartate (D83 in BovRh) does not change the hydrogen-bonding environment in invertebrate rhodopsins. Thus, present FTIR analysis provides specific structural changes, leading to activation of invertebrate and vertebrate rhodopsins. On the other hand, the analysis of O–D stretching vibrations in D2O revealed unique features of protein-bound water molecules. Numbers of water bands in SpiRh1 and SquRh were less and more than those in BovRh. The X-ray crystal structure of SpiRh1 observed a bridged water molecule between the protonated Schiff base and its counterion (E194), but strongly hydrogen-bonded water molecules were never detected in SpiRh1, as well as SquRh and BovRh. Thus, absence of strongly hydrogen-bonded water molecules is substantial for animal rhodopsins, which is distinctive from microbial rhodopsins.

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Section: ■ Resultsmentioning

confidence: 99%

Difference FTIR Spectroscopy of Jumping Spider Rhodopsin-1 at 77 K

et al. 2023

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“…This probably relates to the somewhat different arrangement of the complex counterion and the interaction with the binding pocket residues [102,104]. So far, a blue shift has been observed in all visual iso-pigments tested [101,123], except for the primate blue visual pigment, which apparently cannot stably bind 9-cis retinal [124,125].…”

Section: Isorhodopsin-general Aspectsmentioning

confidence: 96%

Isorhodopsin: An Undervalued Visual Pigment Analog

Grip

Lugtenburg

2022

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Rhodopsin, the first visual pigment identified in the animal retina, was shown to be a photosensitive membrane protein containing covalently bound retinal in the 11-cis configuration, as a chromophore. Upon photoexcitation the chromophore isomerizes in femtoseconds to all-trans, which drives the protein into the active state. Soon thereafter, another geometric isomer—9-cis retinal—was also shown to stably incorporate into the binding pocket, generating a slightly blue-shifted photosensitive protein. This pigment, coined isorhodopsin, was less photosensitive, but could also reach the active state. However, 9-cis retinal was not detected as a chromophore in any of the many animal visual pigments studied, and isorhodopsin was passed over as an exotic and little-relevant rhodopsin analog. Consequently, few in-depth studies of its photochemistry and activation mechanism have been performed. In this review, we aim to illustrate that it is unfortunate that isorhodopsin has received little attention in the visual research and literature. Elementary differences in photoexcitation of rhodopsin and isorhodopsin have already been reported. Further in-depth studies of the photochemical properties and pathways of isorhodopsin would be quite enlightening for the initial steps in vision, as well as being beneficial for biotechnological applications of retinal proteins.

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Light-induced difference FTIR spectroscopy of primate blue-sensitive visual pigment at 163 K

et al. 2021

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Structural studies of color visual pigments lag far behind those of rhodopsin for scotopic vision. Using difference FTIR spectroscopy at 77 K, we report the first structural data of three primate color visual pigments, monkey red (MR), green (MG), and blue (MB), where the batho-intermediate (Batho) exhibits photoequilibrium with the unphotolyzed state. This photochromic property is highly advantageous for limited samples since the signal-to-noise ratio is improved, but may not be applicable to late intermediates, because of large structural changes to proteins. Here we report the photochromic property of MB at 163 K, where the BL intermediate, formed by the relaxation of Batho, is in photoequilibrium with the initial MB state. A comparison of the difference FTIR spectra at 77 and 163 K provided information on what happens in the process of transition from Batho to BL in MB. The coupled C 11 =C 12 HOOP vibration in the planer structure in MB is decoupled by distortion in Batho after retinal photoisomerization, but returns to the coupled C 11 =C 12 HOOP vibration in the all- trans chromophore in BL. The Batho formation accompanies helical structural perturbation, which is relaxed in BL. Protein-bound water molecules that form an extended water cluster near the retinal chromophore change hydrogen bonds differently for Batho and BL, being stronger in the latter than in the initial state. In addition to structural dynamics, the present FTIR spectra show no signals of protonated carboxylic acids at 77 and 163 K, suggesting that E181 is deprotonated in MB, Batho and BL.

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Unique Retinal Binding Pocket of Primate Blue-Sensitive Visual Pigment

Cited by 4 publications

References 52 publications

Difference FTIR Spectroscopy of Jumping Spider Rhodopsin-1 at 77 K

Difference FTIR Spectroscopy of Jumping Spider Rhodopsin-1 at 77 K

Isorhodopsin: An Undervalued Visual Pigment Analog

Light-induced difference FTIR spectroscopy of primate blue-sensitive visual pigment at 163 K

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