Low‐temperature Raman spectroscopy reveals small chromophore distortion in primary photointermediate of proteorhodopsin

Fujisawa, Tomotsumi; Abe, Masahiro; Tamogami, Jun; Kikukawa, Takashi; Kamo, Naoki; Unno, Masashi

doi:10.1002/1873-3468.13219

Cited by 8 publications

(9 citation statements)

References 46 publications

(125 reference statements)

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“…For p HR K , the CC stretching and CH in-plane bending modes exhibit different spectral features from those of p HR hypso and the dark state, which is caused by the isomerization of the chromophore. The intensity patterns of the vibrational bands, including the single-band appearance of the CC stretching modes (∼1200 cm –1 ), were commonly observed in the K intermediate of BR , and proteorhodopsin with the proton-pump activity, and were attributed to the 13- cis form of their retinal chromophores. Importantly, the spectrum of p HR K is characterized by intense HOOP modes.…”

Section: Resultsmentioning

confidence: 98%

Low-Temperature Raman Spectroscopy of Halorhodopsin from Natronomonas pharaonis: Structural Discrimination of Blue-Shifted and Red-Shifted Photoproducts

et al. 2019

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From the low-temperature absorption and Raman measurements of halorhodopsin from Natronomonas pharaonis (pHR), we observed that the two photoproducts were generated after exciting pHR at 80 K by green light. One photoproduct was the red-shifted K intermediate (pHR K ) as the primary photointermediate for Cl − pumping, and the other was the blue-shifted one (pHR hypso ), which was not involved in the Cl − pumping and thermally relaxed to the original unphotolyzed state by increasing temperature. The formation of these two kinds of photoproducts was previously reported for halorhodopsin from Halobacterium sarinarum [Zimanyi et al. Biochemistry 1989, 28, 1656. We found that the same took place in pHR, and we revealed the chromophore structures of the two photointermediates from their Raman spectra for the first time. pHR hypso had the distorted all-trans chromophore, while pHR K contained the distorted 13-cis form. The present results revealed that the structural analyses of pHR K carried out so far at ∼80 K potentially included a significant contribution from pHR hypso . pHR hypso was efficiently formed via the photoexcitation of pHR K , indicating that pHR hypso was likely a side product after photoexcitation of pHR K . The formation of pHR hypso suggested that the active site became tight in pHR K due to the slight movement of Cl − , and the back photoisomerization then produced the distorted all-trans chromophore in pHR hypso .

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Section: Resultsmentioning

confidence: 98%

Low-Temperature Raman Spectroscopy of Halorhodopsin from Natronomonas pharaonis: Structural Discrimination of Blue-Shifted and Red-Shifted Photoproducts

et al. 2019

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“…10-100-fold slower) decay of K compared with that of BR was observed in GPR [105]. Because of such slow K-decay, low-temperature Raman spectroscopic data presented by Fujisawa et al demonstrated that the chromophore structure in GPR in the K state is less distorted compared to that of BR in the same state and is rather close to that of L in BR, which possess a more relaxed chromophore structure [112]. Therefore, the formation of a longer stable K state may obscure the appearance of L in the GPR along with the fast formation of the following M-state.…”

Section: Photocycles Of Other H + -Pumping Rhodopsins Than Brmentioning

confidence: 99%

Functional Mechanism of Proton Pump-Type Rhodopsins Found in Various Microorganisms as a Potential Effective Tool in Optogenetics

Tamogami¹,

Kikukawa²

2022

Epigenetics to Optogenetics - A New Paradigm in the Study of Biology

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Microbial rhodopsins, which are photoreceptive membrane proteins consisting of seven α-helical structural apoproteins (opsin) and a covalently attached retinal chromophore, are one of the most frequently used optogenetic tools. Since the first success of neuronal activation by channelrhodopsin, various microbial rhodopsins functioning as ion channels or pumps have been applied to optogenetics. The use of light-driven ion pumps to generate large negative membrane potentials allows the silencing of neural activity. Although anion-conductive channelrhodopsins have been recently discovered, light-driven outward H+-pumping rhodopsins, which can generate a larger photoinduced current than a light-driven inward Cl−-pump halorhodopsin, must be more efficient tools for this purpose and have been often utilized for optogenetics. There are abundant proton pumps in the microbial world, providing numerous candidates for potential practical optogenetic instruments. In addition, their distinctive features (that is, being accompanied by photoinduced intracellular pH changes) could enable expansion of this technique to versatile applications. Thus, intensive investigation of the molecular mechanisms of various microbial H+-pumps may be useful for the exploration of more potent tools and the creation of effectively designed mutants. In this chapter, we focus on the functional mechanism of microbial H+-pumping rhodopsins. Further, we describe the future prospects of these rhodopsins for optogenetic applications.

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“…A recent Raman study of PR showed that the structure of the RSB chromophore was insensitive to the protonation state of the aspartate near the Schiff base. 8 A small distortion about the Schiff base was also revealed for the initial photointermediate of PR produced at 80K. 8 These observations were attributed to the loose binding site around the Schiff base.…”

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confidence: 97%

Conformational Analysis of a Retinal Schiff Base Chromophore in Proteorhodopsin by Raman Optical Activity

Fujisawa

Nishikawa

Tamogami

et al. 2021

J. Phys. Chem. Lett.

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Raman optical activity (ROA) spectroscopy was used to study the conformation of the retinal Schiff base chromophore in green-light-absorbing proteorhodopsin, which is a globally distributed light-driven proton pump of aquatic bacteria. The ROA spectrum consisted mostly of the negative vibrational bands of the chromophore, while the hydrogen out-of-plane mode (at 960 cm–1) appeared as the sole positive band. This distinct spectral feature was not explained by the twisted structure of the retinal Schiff base but was reproduced by the structural model in which the polyene chain on the β-ionone ring side was bent out-of-plane. The bent chromophore structure potentially couples with proton pumping through the motion of the sixth helix in contact with the β-ionone ring.

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Low‐temperature Raman spectroscopy reveals small chromophore distortion in primary photointermediate of proteorhodopsin

Cited by 8 publications

References 46 publications

Low-Temperature Raman Spectroscopy of Halorhodopsin from Natronomonas pharaonis: Structural Discrimination of Blue-Shifted and Red-Shifted Photoproducts

Low-Temperature Raman Spectroscopy of Halorhodopsin from Natronomonas pharaonis: Structural Discrimination of Blue-Shifted and Red-Shifted Photoproducts

Functional Mechanism of Proton Pump-Type Rhodopsins Found in Various Microorganisms as a Potential Effective Tool in Optogenetics

Conformational Analysis of a Retinal Schiff Base Chromophore in Proteorhodopsin by Raman Optical Activity

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