1
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Shim JG, Kang NR, Chuon K, Cho SG, Meas S, Jung KH. Mutational analyses identify a single amino acid critical for color tuning in proteorhodopsins. FEBS Lett 2022; 596:784-795. [PMID: 35090057 DOI: 10.1002/1873-3468.14297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/08/2022]
Abstract
Microbial rhodopsins are light-activated proteins that contain seven transmembrane alpha-helices. Spectral tuning in microbial rhodopsins is a useful optogenetic tool. In this study, we report a new site that controls spectral tuning. In the proteorhodopsins ISR34 and ISR36, a single amino-acid substitution at Cys189 caused an absorption maximum shift of 44 nm, indicating spectral tuning at a specific site. Comparison of single amino acid substitutions was conducted using photochemical and photobiological approaches. The maximum absorption for red-shift was measured for mutations at positions 189 and 105 in ISR34, both residues being equally important. Structural changes resulting from amino acid substitutions are related to pKa values, pumping activity, and spectral tuning.
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Affiliation(s)
- Jin-Gon Shim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Na-Rae Kang
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Kimleng Chuon
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Shin-Gyu Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Seanghun Meas
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
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2
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Functional Mechanism of Cl --Pump Rhodopsin and Its Conversion into H + Pump. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:55-71. [PMID: 33398807 DOI: 10.1007/978-981-15-8763-4_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Cl--pump rhodopsin is the second discovered microbial rhodopsin. Although its physiological role has not been fully clarified, its functional mechanism has been studied as a model for anion transporters. After the success of neural activation by channel rhodopsin, the first Cl--pump halorhodopsin (HR) had become widely used as a neural silencer. The emergence of artificial and natural anion channel rhodopsins lowered the importance of HRs. However, the longer absorption maxima of approximately 585-600 nm for HRs are still advantageous for applications in mammalian brains and collaborations with neural activators possessing shorter absorption maxima. In this chapter, the variation and functional mechanisms of Cl- pumps are summarized. After the discovery of HR, Cl--pump rhodopsins were confined to only extremely halophilic haloarchaea. However, after 2014, two Cl--pump groups were newly discovered in marine and terrestrial bacteria. These Cl- pumps are phylogenetically distinct from HRs and have unique characteristics. In particular, the most recently identified Cl- pump has close similarity with the H+ pump bacteriorhodopsin and was converted into the H+ pump by a single amino acid replacement.
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3
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Tanaka T, Singh M, Shihoya W, Yamashita K, Kandori H, Nureki O. Structural basis for unique color tuning mechanism in heliorhodopsin. Biochem Biophys Res Commun 2020; 533:262-267. [PMID: 32951839 DOI: 10.1016/j.bbrc.2020.06.124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 10/23/2022]
Abstract
Microbial rhodopsins comprise an opsin protein with seven transmembrane helices and a retinal as the chromophore. An all-trans retinal is covalently bonded to a lysine residue through the retinal Schiff base (RSB) and stabilized by a negatively charged counterion. The distance between the RSB and counterion is closely related to the light energy absorption. However, in heliorhodopsin-48C12 (HeR-48C12), while E107 acts as the counterion, E107D mutation exhibits an identical absorption spectrum to the wild-type, suggesting that the distance does not affect its absorption spectra. Here we present the 2.6 Å resolution crystal structure of the Thermoplasmatales archaeon HeR E108D mutant, which also has an identical absorption spectrum to the wild-type. The structure revealed that D108 does not form a hydrogen bond with the RSB, and its counterion interaction becomes weaker. Alternatively, the serine cluster, S78, S112, and S238 form a distinct interaction network around the RSB. The absorption spectra of the E to D and S to A double mutants suggested that S112 influences the spectral shift by compensating for the weaker counterion interaction. Our structural and spectral studies have revealed the unique spectral shift mechanism of HeR and clarified the physicochemical properties of HeRs.
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Affiliation(s)
- Tatsuki Tanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa, Nagoya, 466-8555, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa, Nagoya, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa, Nagoya, 466-8555, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
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4
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Mantovani V, Hauzman E, Corredor VH, Goulart PRK, Galvão O, Talebi M, Pessoa DMA, Soares JGM, Fiorani M, Gattass R, Fix Ventura D, Bonci DMO. Genetic variability of the sws1 cone opsin gene among New World monkeys. Am J Primatol 2020; 82:e23199. [PMID: 32990997 DOI: 10.1002/ajp.23199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 02/05/2023]
Abstract
Vision is a major sense for Primates and the ability to perceive colors has great importance for the species ecology and behavior. Visual processing begins with the activation of the visual opsins in the retina, and the spectral absorption peaks are highly variable among species. In most Primates, LWS/MWS opsins are responsible for sensitivity to long/middle wavelengths within the visible light spectrum, and SWS1 opsins provide sensitivity to short wavelengths, in the violet region of the spectrum. In this study, we aimed to investigate the genetic variation on the sws1 opsin gene of New World monkeys (NWM) and search for amino acid substitutions that might be associated with the different color vision phenotypes described for a few species. We sequenced the exon 1 of the sws1 opsin gene of seven species from the families Callitrichidae, Cebidae, and Atelidae, and searched for variation at the spectral tuning sites 46, 49, 52, 86, 90, 93, 114, 116, and 118. Among the known spectral tuning sites, only residue 114 was variable. To investigate whether other residues have a functional role in the SWS1 absorption peak, we performed computational modeling of wild-type SWS1 and mutants A50I and A50V, found naturally among the species investigated. Although in silico analysis did not show any visible effect caused by these substitutions, it is possible that interactions of residue 50 with other sites might have some effect in the spectral shifts in the order of ~14 nm, found among the NWM. We also performed phylogenetic reconstruction of the sws1 gene, which partially recovered the species phylogeny. Further studies will be important to uncover the mutations responsible for the phenotypic variability of the SWS1 of NWM, and how spectral tuning may be associated with specific ecological features such as preferred food items and habitat use.
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Affiliation(s)
- Viviani Mantovani
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Einat Hauzman
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
| | - Vitor H Corredor
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Paulo R K Goulart
- Núcleo de Teoria de Pesquisa do Comportamento, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Olavo Galvão
- Núcleo de Teoria de Pesquisa do Comportamento, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Mauricio Talebi
- Departamento de Ciências Ambientais, Universidade Federal de São Paulo, Campus Diadema, São Paulo, São Paulo, Brazil
| | - Daniel M A Pessoa
- Departamento de Fisiologia e Comportamento, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Juliana G M Soares
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mario Fiorani
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo Gattass
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dora Fix Ventura
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
| | - Daniela M O Bonci
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
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5
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Singh M, Katayama K, Béjà O, Kandori H. Anion binding to mutants of the Schiff base counterion in heliorhodopsin 48C12. Phys Chem Chem Phys 2019; 21:23663-23671. [DOI: 10.1039/c9cp04102h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The anion binds as the direct H-bonding acceptor of the Schiff base in E107A, while E107Q indirectly accommodates an anion.
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Affiliation(s)
- Manish Singh
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBioTechnology Research Center
| | - Oded Béjà
- Faculty of Biology
- Technion – Israel Institute of Technology
- Haifa
- Israel
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBioTechnology Research Center
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6
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Understanding Colour Tuning Rules and Predicting Absorption Wavelengths of Microbial Rhodopsins by Data-Driven Machine-Learning Approach. Sci Rep 2018; 8:15580. [PMID: 30349075 PMCID: PMC6197263 DOI: 10.1038/s41598-018-33984-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 10/07/2018] [Indexed: 11/09/2022] Open
Abstract
The light-dependent ion-transport function of microbial rhodopsin has been widely used in optogenetics for optical control of neural activity. In order to increase the variety of rhodopsin proteins having a wide range of absorption wavelengths, the light absorption properties of various wild-type rhodopsins and their artificially mutated variants were investigated in the literature. Here, we demonstrate that a machine-learning-based (ML-based) data-driven approach is useful for understanding and predicting the light-absorption properties of microbial rhodopsin proteins. We constructed a database of 796 proteins consisting of microbial rhodopsin wildtypes and their variants. We then proposed an ML method that produces a statistical model describing the relationship between amino-acid sequences and absorption wavelengths and demonstrated that the fitted statistical model is useful for understanding colour tuning rules and predicting absorption wavelengths. By applying the ML method to the database, two residues that were not considered in previous studies are newly identified to be important to colour shift.
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7
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Tan YL, Mitchell J, Klein-Seetharaman J, Nietlispach D. Characterization of Denatured States and Reversible Unfolding of Sensory Rhodopsin II. J Mol Biol 2018; 430:4068-4086. [PMID: 30098339 DOI: 10.1016/j.jmb.2018.07.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/16/2018] [Accepted: 07/23/2018] [Indexed: 12/27/2022]
Abstract
Our understanding on the folding of membrane proteins lags behind that of soluble proteins due to challenges posed by the exposure of hydrophobic regions during in vitro chemical denaturation and refolding experiments. While different folding models are accepted for soluble proteins, only the two-stage model and the long-range interactions model have been proposed so far for helical membrane proteins. To address our knowledge gap on how different membrane proteins traverse their folding pathways, we have systematically investigated the structural features of SDS-denatured states and the kinetics for reversible unfolding of sensory rhodopsin II (pSRII), a retinal-binding photophobic receptor from Natronomonas pharaonis. pSRII is difficult to denature, and only SDS can dislodge the retinal chromophore without rapid aggregation. Even in 30% SDS (0.998 ΧSDS), pSRII retains the equivalent of six out of seven transmembrane helices, while the retinal-binding pocket is disrupted, with transmembrane residues becoming more solvent exposed. Folding of pSRII from an SDS-denatured state harboring a covalently bound retinal chromophore shows deviations from an apparent two-state behavior. SDS denaturation to form the sensory opsin apo-protein is reversible. We report pSRII as a new model protein which is suitable for membrane protein folding studies and has a unique folding mechanism that differs from those of bacteriorhodopsin and bovine rhodopsin.
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Affiliation(s)
- Yi Lei Tan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom
| | - James Mitchell
- Biomedical Sciences Division, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Judith Klein-Seetharaman
- Biomedical Sciences Division, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, United Kingdom.
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8
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Collette F, Renger T, Müh F, Schmidt am Busch M. Red/Green Color Tuning of Visual Rhodopsins: Electrostatic Theory Provides a Quantitative Explanation. J Phys Chem B 2018; 122:4828-4837. [DOI: 10.1021/acs.jpcb.8b02702] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florimond Collette
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Frank Müh
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Marcel Schmidt am Busch
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
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9
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Fujimoto K, Hayashi S, Hasegawa JY, Nakatsuji H. Theoretical Studies on the Color-Tuning Mechanism in Retinal Proteins. J Chem Theory Comput 2015; 3:605-18. [PMID: 26637039 DOI: 10.1021/ct6002687] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The excited states of the three retinal proteins, bovine rhodopsin (Rh), bacteriorhodopsin (bR), and sensory rhodopsin II (sRII) were studied using the symmetry-adapted cluster-configuration interaction (SAC-CI) and combined quantum mechanical and molecular mechanical (QM/MM) methods. The computed absorption energies are in good agreement with the experimental ones for all three proteins. The spectral tuning mechanism was analyzed in terms of three contributions: molecular structures of the chromophore in the binding pockets, electrostatic (ES) interaction of the chromophore with the surrounding protein environment, and quantum-mechanical effect between the chromophore and the counterion group. This analysis provided an insight into the mechanism of the large blue-shifts in the absorption peak position of Rh and sRII from that of bR. Protein ES effect is primarily important both in Rh and in sRII, and the structure effect is secondary important in Rh. The quantum-mechanical interaction between the chromophore and the counterion is very important for quantitative reproduction of the excitation energy. These results indicate that the present approach is useful for studying the absorption spectra and the mechanism of the color tuning in the retinal proteins.
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Affiliation(s)
- Kazuhiro Fujimoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyou-ku, Kyoto 615-8510, Japan, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyou-ku, Kyoto 606-8520, Japan, and Quantum Chemistry Research Institute (QCRI), 58-8 Mikawa, Momoyama-cho, Fushimi-ku, Kyoto 612-8029, Japan
| | - Shigehiko Hayashi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyou-ku, Kyoto 615-8510, Japan, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyou-ku, Kyoto 606-8520, Japan, and Quantum Chemistry Research Institute (QCRI), 58-8 Mikawa, Momoyama-cho, Fushimi-ku, Kyoto 612-8029, Japan
| | - Jun-Ya Hasegawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyou-ku, Kyoto 615-8510, Japan, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyou-ku, Kyoto 606-8520, Japan, and Quantum Chemistry Research Institute (QCRI), 58-8 Mikawa, Momoyama-cho, Fushimi-ku, Kyoto 612-8029, Japan
| | - Hiroshi Nakatsuji
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyou-ku, Kyoto 615-8510, Japan, PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyou-ku, Kyoto 606-8520, Japan, and Quantum Chemistry Research Institute (QCRI), 58-8 Mikawa, Momoyama-cho, Fushimi-ku, Kyoto 612-8029, Japan
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10
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Inoue K, Koua FHM, Kato Y, Abe-Yoshizumi R, Kandori H. Spectroscopic study of a light-driven chloride ion pump from marine bacteria. J Phys Chem B 2014; 118:11190-9. [PMID: 25166488 DOI: 10.1021/jp507219q] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Thousands of light-driven proton-pumping rhodopsins have been found in marine microbes, and a light-driven sodium-ion pumping rhodopsin was recently discovered, which utilizes sunlight for the energy source of the cell. Similarly, a light-driven chloride-ion pump has been found from marine bacteria, and three eubacterial light-driven pumps possess the DTE (proton pump), NDQ (sodium-ion pump), and NTQ (chloride-ion pump) motifs corresponding to the D85, T89, and D96 positions in bacteriorhodopsin (BR). The corresponding motif of the known haloarchaeal chloride-ion pump, halorhodopsin (HR), is TSA, which is entirely different from the NTQ motif of a eubacterial chloride-ion pump. It is thus intriguing to compare the molecular mechanism of these two chloride-ion pumps. Here we report the spectroscopic study of Fulvimarina rhodopsin (FR), a eubacterial light-driven chloride-ion pump from marine bacterium. FR binds a chloride-ion near the retinal chromophore and chloride-ion binding causes a spectral blue-shift. FR predominantly possesses an all-trans retinal, which is responsible for the light-driven chloride-ion pump. Upon light absorption, the red-shifted K intermediate is formed, followed by the appearance of the L and O intermediates. When the M intermediate does not form, this indicates that the Schiff base remains in the protonated state during the photocycle. These molecular mechanisms are common in HR, and a common mechanism for chloride-ion pumping by evolutionarily distant proteins suggests the importance of the electric quadrupole in the Schiff base region and their changes through hydrogen-bonding alterations. One noticeable difference between FR and HR is the uptake of chloride-ion from the extracellular surface. While the uptake occurs upon decay of the O intermediate in HR, chloride-ion uptake accompanies the rise of the O intermediate in FR. This suggests the presence of a second chloride-ion binding site near the extracellular surface of FR, which is unique to the NTQ rhodopsin.
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Affiliation(s)
- Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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11
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Hauser FE, van Hazel I, Chang BSW. Spectral tuning in vertebrate short wavelength-sensitive 1 (SWS1) visual pigments: Can wavelength sensitivity be inferred from sequence data? JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:529-39. [DOI: 10.1002/jez.b.22576] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 03/05/2014] [Accepted: 05/06/2014] [Indexed: 01/12/2023]
Affiliation(s)
- Frances E. Hauser
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario Canada
| | - Ilke van Hazel
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario Canada
| | - Belinda S. W. Chang
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario Canada
- Department of Cell & Systems Biology; University of Toronto; Toronto Ontario Canada
- Centre for the Analysis of Genome Evolution & Function; University of Toronto; Toronto Ontario Canada
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12
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Mehler M, Scholz F, Ullrich SJ, Mao J, Braun M, Brown LJ, Brown RCD, Fiedler SA, Becker-Baldus J, Wachtveitl J, Glaubitz C. The EF loop in green proteorhodopsin affects conformation and photocycle dynamics. Biophys J 2014; 105:385-97. [PMID: 23870260 DOI: 10.1016/j.bpj.2013.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/10/2013] [Accepted: 06/11/2013] [Indexed: 11/20/2022] Open
Abstract
The proteorhodopsin family consists of retinal proteins of marine bacterial origin with optical properties adjusted to their local environments. For green proteorhodopsin, a highly specific mutation in the EF loop, A178R, has been found to cause a surprisingly large redshift of 20 nm despite its distance from the chromophore. Here, we analyze structural and functional consequences of this EF loop mutation by time-resolved optical spectroscopy and solid-state NMR. We found that the primary photoreaction and the formation of the K-like photo intermediate is almost pH-independent and slower compared to the wild-type, whereas the decay of the K-intermediate is accelerated, suggesting structural changes within the counterion complex upon mutation. The photocycle is significantly elongated mainly due to an enlarged lifetime of late photo intermediates. Multidimensional MAS-NMR reveals mutation-induced chemical shift changes propagating from the EF loop to the chromophore binding pocket, whereas dynamic nuclear polarization-enhanced (13)C-double quantum MAS-NMR has been used to probe directly the retinylidene conformation. Our data show a modified interaction network between chromophore, Schiff base, and counterion complex explaining the altered optical and kinetic properties. In particular, the mutation-induced distorted structure in the EF loop weakens interactions, which help reorienting helix F during the reprotonation step explaining the slower photocycle. These data lead to the conclusion that the EF loop plays an important role in proton uptake from the cytoplasm but our data also reveal a clear interaction pathway between the EF loop and retinal binding pocket, which might be an evolutionary conserved communication pathway in retinal proteins.
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Affiliation(s)
- Michaela Mehler
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, Germany
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13
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Bassolino G, Sovdat T, Liebel M, Schnedermann C, Odell B, Claridge TD, Kukura P, Fletcher SP. Synthetic Control of Retinal Photochemistry and Photophysics in Solution. J Am Chem Soc 2014; 136:2650-8. [DOI: 10.1021/ja4121814] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giovanni Bassolino
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Tina Sovdat
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Matz Liebel
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Christoph Schnedermann
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Barbara Odell
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Timothy D.W. Claridge
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Philipp Kukura
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Stephen P. Fletcher
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
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14
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Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown L, Kandori H. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 2014; 114:126-63. [PMID: 24364740 PMCID: PMC3979449 DOI: 10.1021/cr4003769] [Citation(s) in RCA: 770] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Oliver P. Ernst
- Departments
of Biochemistry and Molecular Genetics, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Toronto, Ontario M5S 1A8, Canada
| | - David T. Lodowski
- Center
for Proteomics and Bioinformatics, Case
Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Marcus Elstner
- Institute
for Physical Chemistry, Karlsruhe Institute
of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Peter Hegemann
- Institute
of Biology, Experimental Biophysics, Humboldt-Universität
zu Berlin, Invalidenstrasse
42, 10115 Berlin, Germany
| | - Leonid
S. Brown
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Hideki Kandori
- Department
of Frontier Materials, Nagoya Institute
of Technology, Showa-ku, Nagoya 466-8555, Japan
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15
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16
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Imamoto Y, Shichida Y. Cone visual pigments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:664-73. [PMID: 24021171 DOI: 10.1016/j.bbabio.2013.08.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/07/2013] [Accepted: 08/30/2013] [Indexed: 12/16/2022]
Abstract
Cone visual pigments are visual opsins that are present in vertebrate cone photoreceptor cells and act as photoreceptor molecules responsible for photopic vision. Like the rod visual pigment rhodopsin, which is responsible for scotopic vision, cone visual pigments contain the chromophore 11-cis-retinal, which undergoes cis-trans isomerization resulting in the induction of conformational changes of the protein moiety to form a G protein-activating state. There are multiple types of cone visual pigments with different absorption maxima, which are the molecular basis of color discrimination in animals. Cone visual pigments form a phylogenetic sister group with non-visual opsin groups such as pinopsin, VA opsin, parapinopsin and parietopsin groups. Cone visual pigments diverged into four groups with different absorption maxima, and the rhodopsin group diverged from one of the four groups of cone visual pigments. The photochemical behavior of cone visual pigments is similar to that of pinopsin but considerably different from those of other non-visual opsins. G protein activation efficiency of cone visual pigments is also comparable to that of pinopsin but higher than that of the other non-visual opsins. Recent measurements with sufficient time-resolution demonstrated that G protein activation efficiency of cone visual pigments is lower than that of rhodopsin, which is one of the molecular bases for the lower amplification of cones compared to rods. In this review, the uniqueness of cone visual pigments is shown by comparison of their molecular properties with those of non-visual opsins and rhodopsin. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Yasushi Imamoto
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshinori Shichida
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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17
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Sudo Y, Okazaki A, Ono H, Yagasaki J, Sugo S, Kamiya M, Reissig L, Inoue K, Ihara K, Kandori H, Takagi S, Hayashi S. A blue-shifted light-driven proton pump for neural silencing. J Biol Chem 2013; 288:20624-32. [PMID: 23720753 DOI: 10.1074/jbc.m113.475533] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ion-transporting rhodopsins are widely utilized as optogenetic tools both for light-induced neural activation and silencing. The most studied representative is Bacteriorhodopsin (BR), which absorbs green/red light (∼570 nm) and functions as a proton pump. Upon photoexcitation, BR induces a hyperpolarization across the membrane, which, if incorporated into a nerve cell, results in its neural silencing. In this study, we show that several residues around the retinal chromophore, which are completely conserved among BR homologs from the archaea, are involved in the spectral tuning in a BR homolog (HwBR) and that the combination mutation causes a large spectral blue shift (λmax = 498 nm) while preserving the robust pumping activity. Quantum mechanics/molecular mechanics calculations revealed that, compared with the wild type, the β-ionone ring of the chromophore in the mutant is rotated ∼130° because of the lack of steric hindrance between the methyl groups of the retinal and the mutated residues, resulting in the breakage of the π conjugation system on the polyene chain of the retinal. By the same mutations, similar spectral blue shifts are also observed in another BR homolog, archearhodopsin-3 (also called Arch). The color variant of archearhodopsin-3 could be successfully expressed in the neural cells of Caenorhabditis elegans, and illumination with blue light (500 nm) led to the effective locomotory paralysis of the worms. Thus, we successfully produced a blue-shifted proton pump for neural silencing.
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Affiliation(s)
- Yuki Sudo
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.
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18
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Rajamani R, Lin YL, Gao J. The opsin shift and mechanism of spectral tuning in rhodopsin. J Comput Chem 2011; 32:854-65. [PMID: 20941732 PMCID: PMC3021771 DOI: 10.1002/jcc.21663] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 08/07/2010] [Indexed: 01/12/2023]
Abstract
Molecular dynamics simulations and combined quantum mechanical and molecular mechanical calculations have been performed to investigate the mechanism of the opsin shift and spectral tuning in rhodopsin. A red shift of -980 cm(-1) was estimated in the transfer of the chromophore from methanol solution environment to the protonated Schiff base (PSB)-binding site of the opsin. The conformational change from a 6-s-cis-all-trans configuration in solution to the 6-s-cis-11-cis conformer contributes additional -200 cm(-1), and the remaining effects were attributed to dispersion interactions with the aromatic residues in the binding site. An opsin shift of 2100 cm(-1) was obtained, in reasonable accord with experiment (2730 cm(-1)). Dynamics simulations revealed that the 6-s-cis bond can occupy two main conformations for the β-ionone ring, resulting in a weighted average dihedral angle of about -50°, which may be compared with the experimental estimate of -28° from solid-state NMR and Raman data. We investigated a series of four single mutations, including E113D, A292S, T118A, and A269T, which are located near the PSB, along the polyene chain of retinal and close to the ionone ring. The computational results on absorption energy shift provided insights into the mechanism of spectral tuning, which involves all means of electronic structural effects, including the stabilization or destabilization of either the ground or the electronically excited state of the retinal PSB.
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Affiliation(s)
| | - Yen-lin Lin
- Department of Chemistry, Digital Technology Center, and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
| | - Jiali Gao
- Department of Chemistry, Digital Technology Center, and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
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19
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Sudo Y, Yuasa Y, Shibata J, Suzuki D, Homma M. Spectral tuning in sensory rhodopsin I from Salinibacter ruber. J Biol Chem 2011; 286:11328-36. [PMID: 21288897 DOI: 10.1074/jbc.m110.187948] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Organisms utilize light as energy sources and as signals. Rhodopsins, which have seven transmembrane α-helices with retinal covalently linked to a conserved Lys residue, are found in various organisms as distant in evolution as bacteria, archaea, and eukarya. One of the most notable properties of rhodopsin molecules is the large variation in their absorption spectrum. Sensory rhodopsin I (SRI) and sensory rhodopsin II (SRII) function as photosensors and have similar properties (retinal composition, photocycle, structure, and function) except for their λ(max) (SRI, ∼560 nm; SRII, ∼500 nm). An expression system utilizing Escherichia coli and the high protein stability of a newly found SRI-like protein, SrSRI, enables studies of mutant proteins. To determine the residue contributing to the spectral shift from SRI to SRII, we constructed various SRI mutants, in which individual residues were substituted with the corresponding residues of SRII. Three such mutants of SrSRI showed a large spectral blue-shift (>14 nm) without a large alteration of their retinal composition. Two of them, A136Y and A200T, are newly discovered color tuning residues. In the triple mutant, the λ(max) was 525 nm. The inverse mutation of SRII (F134H/Y139A/T204A) generated a spectral-shifted SRII toward longer wavelengths, although the effect is smaller than in the case of SRI, which is probably due to the lack of anion binding in the SRII mutant. Thus, half of the spectral shift from SRI to SRII could be explained by only those three residues taking into account the effect of Cl(-) binding.
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Affiliation(s)
- Yuki Sudo
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan.
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20
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Mori T, Nakano K, Kato S. Conical intersections of free energy surfaces in solution: Effect of electron correlation on a protonated Schiff base in methanol solution. J Chem Phys 2010; 133:064107. [DOI: 10.1063/1.3472033] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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21
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Suzuki D, Irieda H, Homma M, Kawagishi I, Sudo Y. Phototactic and chemotactic signal transduction by transmembrane receptors and transducers in microorganisms. SENSORS 2010; 10:4010-39. [PMID: 22319339 PMCID: PMC3274258 DOI: 10.3390/s100404010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 03/29/2010] [Accepted: 04/09/2010] [Indexed: 12/17/2022]
Abstract
Microorganisms show attractant and repellent responses to survive in the various environments in which they live. Those phototaxic (to light) and chemotaxic (to chemicals) responses are regulated by membrane-embedded receptors and transducers. This article reviews the following: (1) the signal relay mechanisms by two photoreceptors, Sensory Rhodopsin I (SRI) and Sensory Rhodopsin II (SRII) and their transducers (HtrI and HtrII) responsible for phototaxis in microorganisms; and (2) the signal relay mechanism of a chemoreceptor/transducer protein, Tar, responsible for chemotaxis in E. coli. Based on results mainly obtained by our group together with other findings, the possible molecular mechanisms for phototaxis and chemotaxis are discussed.
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Affiliation(s)
- Daisuke Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan; E-Mails: (D.S.); (H.I.); (M.H.)
| | - Hiroki Irieda
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan; E-Mails: (D.S.); (H.I.); (M.H.)
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan; E-Mails: (D.S.); (H.I.); (M.H.)
| | - Ikuro Kawagishi
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, 184-8584, Japan; E-Mail: (I.K.)
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, 184-8584, Japan
| | - Yuki Sudo
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan; E-Mails: (D.S.); (H.I.); (M.H.)
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-52-789-2993; Fax: +81-52-789-3001
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22
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Rajput J, Rahbek D, Andersen L, Hirshfeld A, Sheves M, Altoè P, Orlandi G, Garavelli M. Probing and Modeling the Absorption of Retinal Protein Chromophores in Vacuo. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Rajput J, Rahbek D, Andersen L, Hirshfeld A, Sheves M, Altoè P, Orlandi G, Garavelli M. Probing and Modeling the Absorption of Retinal Protein Chromophores in Vacuo. Angew Chem Int Ed Engl 2010; 49:1790-3. [DOI: 10.1002/anie.200905061] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Watanabe HC, Mori Y, Tada T, Yokoyama S, Yamato T. Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin. Biophysics (Nagoya-shi) 2010; 6:67-68. [PMID: 21297892 PMCID: PMC3032607 DOI: 10.2142/biophysics.6.67] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The synergetic effects of multiple rhodopsin mutations on color tuning need to be completely elucidated. Systematic genetic studies and spectroscopy have demonstrated an interesting example of synergetic color tuning between two amino acid residues in conger rhodopsin's ancestral pigment (p501): -a double mutation at one nearby and one distant residue led to a significant λ(max) blue shift of 13 nm, whereas neither of the single mutations at these two sites led to meaningful shifts.To analyze the molecular mechanisms of this synergetic color tuning, we performed homology modeling, molecular simulations, and electronic state calculations. For the double mutant, N195A/A292S, in silico mutation analysis demonstrated conspicuous structural changes in the retinal chromophore, whereas that of the single mutant, A292S, was almost unchanged. Using statistical ensembles of QM/MM optimized structures, the excitation energy of retinal chromophore was evaluated for the three visual pigments. As a result, the λ(max) shift of double mutant (DM) from p501 was -8 nm, while that of single mutant (SM) from p501 was +1 nm. Molecular dynamics simulation for DM demonstrated frequent isomerization between 6-s-cis and 6-s-trans conformers. Unexpectedly, however, the two conformers exhibited almost identical excitation energy, whereas principal component analysis (PCA) identified the retinal-counterion cooperative change of BLA (bond length alternation) and retinal-counterion interaction lead to the shift.
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Affiliation(s)
- Hiroshi C Watanabe
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
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25
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Suzuki D, Furutani Y, Inoue K, Kikukawa T, Sakai M, Fujii M, Kandori H, Homma M, Sudo Y. Effects of chloride ion binding on the photochemical properties of salinibacter sensory rhodopsin I. J Mol Biol 2009; 392:48-62. [PMID: 19560470 DOI: 10.1016/j.jmb.2009.06.050] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 05/31/2009] [Accepted: 06/18/2009] [Indexed: 10/20/2022]
Abstract
Microbial organisms utilize light not only as energy sources but also as signals by which rhodopsins (containing retinal as a chromophore) work as photoreceptors. Sensory rhodopsin I (SRI) is a dual photoreceptor that regulates both negative and positive phototaxis in microbial organisms, such as the archaeon Halobacterium salinarum and the eubacterium Salinibacter ruber. These organisms live in highly halophilic environments, suggesting the possibility of the effects of salts on the function of SRI. However, such effects remain unclear because SRI proteins from H. salinarum (HsSRI) are unstable in dilute salt solutions. Recently, we characterized a new SRI protein (SrSRI) that is stable even in the absence of salts, thus allowing us to investigate the effects of salts on the photochemical properties of SRI. In this study, we report that the absorption maximum of SrSRI is shifted from 542 to 556 nm in a Cl(-)-dependent manner with a K(m) of 307+/-56 mM, showing that Cl(-)-binding sites exist in SRI. The bathochromic shift was caused not only by NaCl but also by other salts (NaI, NaBr, and NaNO(3)), implying that I(-), Br(-), and NO(3)(-) can also bind to SrSRI. In addition, the photochemical properties during the photocycle are also affected by chloride ion binding. Mutagenesis studies strongly suggested that a conserved residue, His131, is involved in the Cl(-)-binding site. In light of these results, we discuss the effects of the Cl(-) binding to SRI and the roles of Cl(-) binding in its function.
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26
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Gansmüller A, Concistrè M, McLean N, Johannessen OG, Marín-Montesinos I, Bovee-Geurts PHM, Verdegem P, Lugtenburg J, Brown RCD, Degrip WJ, Levitt MH. Towards an interpretation of 13C chemical shifts in bathorhodopsin, a functional intermediate of a G-protein coupled receptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1350-7. [PMID: 19265671 DOI: 10.1016/j.bbamem.2009.02.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 02/13/2009] [Accepted: 02/18/2009] [Indexed: 10/21/2022]
Abstract
Photoisomerization of the membrane-bound light receptor protein rhodopsin leads to an energy-rich photostate called bathorhodopsin, which may be trapped at temperatures of 120 K or lower. We recently studied bathorhodopsin by low-temperature solid-state NMR, using in situ illumination of the sample in a purpose-built NMR probe. In this way we acquired (13)C chemical shifts along the retinylidene chain of the chromophore. Here we compare these results with the chemical shifts of the dark state chromophore in rhodopsin, as well as with the chemical shifts of retinylidene model compounds in solution. An earlier solid-state NMR study of bathorhodopsin found only small changes in the (13)C chemical shifts upon isomerization, suggesting only minor perturbations of the electronic structure in the isomerized retinylidene chain. This is at variance with our recent measurements which show much larger perturbations of the (13)C chemical shifts. Here we present a tentative interpretation of our NMR results involving an increased charge delocalization inside the polyene chain of the bathorhodopsin chromophore. Our results suggest that the bathochromic shift of bathorhodopsin is due to modified electrostatic interactions between the chromophore and the binding pocket, whereas both electrostatic interactions and torsional strain are involved in the energy storage mechanism of bathorhodopsin.
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Affiliation(s)
- Axel Gansmüller
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, England, UK
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27
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Nielsen MB. Model systems for understanding absorption tuning by opsin proteins. Chem Soc Rev 2009; 38:913-24. [DOI: 10.1039/b802068j] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Bauer M, Rollberg A, Barth A, Spange S. Differentiating Between Dipolarity and Polarizability Effects of Solvents Using the Solvatochromism of Barbiturate Dyes. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800355] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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29
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Singh AK, Hota PK. Development of Bacteriorhodopsin Analogues and Studies of Charge Separated Excited States in the Photoprocesses of Linear Polyenes†. Photochem Photobiol 2007; 83:50-62. [PMID: 16872254 DOI: 10.1562/2006-03-11-ir-844] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Development of bacteriorhodopsin (bR) analogues employing chromophore substitution technique for the purpose of characterizing the binding site of bR and generating bR analogues with novel opto-electronic properties for applications as photoactive element in nanotechnical devices are described. Additionally, the photophysical and photochemical properties of variously substituted diarylpolyenes as models of photobiologically relevant linear polyenes are discussed. The role of charge separated dipolar excited states in the photoprocesses of linear polyenes is highlighted.
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Affiliation(s)
- Anil K Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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30
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Bismuth O, Friedman N, Sheves M, Ruhman S. Photochemistry of a Retinal Protonated Schiff-Base Analogue Mimicking the Opsin Shift of Bacteriorhodopsin. J Phys Chem B 2007; 111:2327-34. [PMID: 17298090 DOI: 10.1021/jp0669308] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A retinal Schiff base analogue which artificially mimics the protein-induced red shifting of absorption in bacteriorhodopsin (BR) has been investigated with femtosecond multichannel pump probe spectroscopy. The objective is to determine if the catalysis of retinal internal conversion in the native protein BR, which absorbs at 570 nm, is directly correlated with the protein-induced Stokes shifting of this absorption band otherwise known as the "opsin shift". Results demonstrate that the red shift afforded in the model system does not hasten internal conversion relative to that taking place in a free retinal-protonated Schiff base (RPSB) in methanol solution, and stimulated emission takes place with biexponential kinetics and characteristic timescales of approximately 2 and 10.5 ps. This shows that interactions between the prosthetic group and the protein that lead to the opsin shift in BR are not directly involved in reducing the excited-state lifetime by nearly an order of magnitude. A sub-picosecond phase of spectral evolution, analogues of which are detected in photoexcited retinal proteins and RPSBs in solution, is observed after excitation anywhere within the intense visible absorption band. It consists of a large and discontinuous spectral shift in excited-state absorption and is assigned to electronic relaxation between excited states, a scenario which might also be relevant to those systems as well. Finally, a transient excess bleach component that tunes with the excitation wavelength is detected in the data and tentatively assigned to inhomogeneous broadening in the ground state absorption band. Possible sources of such inhomogeneity and its relevance to native RPSB photochemistry are discussed.
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Affiliation(s)
- Oshrat Bismuth
- Department of Physical Chemistry, Hebrew University, Jerusalem 91904, Israel
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31
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32
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Sonnewald U, Seltzer S. Synthesis of 3,7-dimethyl-9-(4′-(3H-diazirinyl)-2′,6′-dimethylphenyl)-2E, 4E, 6E, 8E-nonatetraenal-1-3H, A photoaffinity labeling analogue of all-trans-retinal. J Labelled Comp Radiopharm 2006. [DOI: 10.1002/jlcr.2580240709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Sekharan S, Weingart O, Buss V. Ground and excited states of retinal schiff base chromophores by multiconfigurational perturbation theory. Biophys J 2006; 91:L07-9. [PMID: 16648170 PMCID: PMC1479055 DOI: 10.1529/biophysj.106.087122] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Accepted: 04/25/2006] [Indexed: 11/18/2022] Open
Abstract
We have studied the wavelength dependence of retinal Schiff base absorbencies on the protonation state of the chromophore at the multiconfigurational level of theory using second order perturbation theory (CASPT2) within an atomic natural orbital basis set on MP2 optimized geometries. Quantitative agreement between calculated and experimental absorption maxima was obtained for protonated and deprotonated Schiff bases of all-trans- and 11-cis-retinal and intermediate states covering a wavelength range from 610 to 353 nm. These data will be useful as reference points for the calibration of more approximate schemes.
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Affiliation(s)
- Sivakumar Sekharan
- Department of Chemistry, University of Duisburg-Essen, Campus Duisburg, D-47048 Duisburg, Germany
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34
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Kloppmann E, Becker T, Ullmann GM. Electrostatic potential at the retinal of three archaeal rhodopsins: implications for their different absorption spectra. Proteins 2006; 61:953-65. [PMID: 16247786 DOI: 10.1002/prot.20744] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The color tuning mechanism of the rhodopsin protein family has been in the focus of research for decades. However, the structural basis of the tuning mechanism in general and of the absorption shift between rhodopsins in particular remains under discussion. It is clear that a major determinant for spectral shifts between different rhodopsins are electrostatic interactions between the chromophore retinal and the protein. Based on the Poisson-Boltzmann equation, we computed and compared the electrostatic potential at the retinal of three archaeal rhodopsins: bacteriorhodopsin (BR), halorhodopsin (HR), and sensory rhodopsin II (SRII) for which high-resolution structures are available. These proteins are an excellent test case for understanding the spectral tuning of retinal. The absorption maxima of BR and HR are very similar, whereas the spectrum of SRII is considerably blue shifted--despite the structural similarity between these three proteins. In agreement with their absorption maxima, we find that the electrostatic potential is similar in BR and HR, whereas significant differences are seen for SRII. The decomposition of the electrostatic potential into contributions of individual residues, allowed us to identify seven residues that are responsible for the differences in electrostatic potential between the proteins. Three of these residues are located in the retinal binding pocket and have in fact been shown to account for part of the absorption shift between BR and SRII by mutational studies. One residue is located close to the beta-ionone ring of retinal and the remaining three residues are more than 8 A away from the retinal. These residues have not been discussed before, because they are, partly because of their location, no obvious candidates for the spectral shift among BR, HR, and SRII. However, their contribution to the differences in electrostatic potential is evident. The counterion of the Schiff base, which is frequently discussed to be involved in the spectral tuning, does not contribute to the dissimilarities between the electrostatic potentials.
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Affiliation(s)
- Edda Kloppmann
- Structural Biology/Bioinformatics, University of Bayreuth, Bayreuth, Germany
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35
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Röhrig UF, Guidoni L, Rothlisberger U. Solvent and Protein Effects on the Structure and Dynamics of the Rhodopsin Chromophore. Chemphyschem 2005; 6:1836-47. [PMID: 16110519 DOI: 10.1002/cphc.200500066] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The structure and dynamics of the retinal chromophore of rhodopsin are investigated systematically in different environments (vacuum, methanol solution, and protein binding pocket) and with different computational approaches (classical, quantum, and hybrid quantum mechanics/molecular mechanics (QM/MM) descriptions). Finite temperature effects are taken into account by molecular dynamics simulations. The different components that determine the structure and dynamics of the chromophore in the protein are dissected, both in the dark state and in the early photointermediates. In vacuum and in solution the chromophore displays a very high flexibility, which is significantly reduced by the protein environment. In the 11-cis chromophore, the bond-length alternation, which is correlated with the dipole moment, is found to be similar in solution and in the protein, while it differs greatly with respect to minimum-energy vacuum structures. In the model of the earliest protein photointermediate, the highly twisted chromophore shows a very reduced bond-length alternation.
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Affiliation(s)
- Ute F Röhrig
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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36
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Cembran A, Bernardi F, Olivucci M, Garavelli M. The retinal chromophore/chloride ion pair: structure of the photoisomerization path and interplay of charge transfer and covalent states. Proc Natl Acad Sci U S A 2005; 102:6255-60. [PMID: 15855270 PMCID: PMC1088357 DOI: 10.1073/pnas.0408723102] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ab initio multi-reference second-order perturbation theory computations are used to explore the photochemical behavior of two ion pairs constituted by a chloride counterion interacting with either a rhodopsin or bacteriorhodopsin chromophore model (i.e., the 4-cis-gamma-methylnona-2,4,6,8-tetraeniminium and all-trans-nona-2,4,6,8-tetraeniminium cations, respectively). Significant counterion effects on the structure of the photoisomerization paths are unveiled by comparison with the paths of the same chromophores in vacuo. Indeed, we demonstrate that the counterion (i) modulates the relative stability of the S0, S1, and S2 energy surfaces leading to an S1 isomerization energy profile where the S1 and S2 states are substantially degenerate; (ii) leads to the emergence of significant S1 energy barriers along all of the isomerization paths except the one mimicking the 11-cis --> all-trans isomerization of the rhodopsin chromophore model; and (iii) changes the nature of the S1 --> S0 decay funnel that becomes a stable excited state minimum when the isomerizing double bond is located at the center of the chromophore moiety. We show that these (apparently very different) counterion effects can be rationalized on the basis of a simple qualitative electrostatic model, which also provides a crude basis for understanding the behavior of retinal protonated Schiff bases in solution.
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Affiliation(s)
- Alessandro Cembran
- Dipartimento di Chimica G. Ciamician, Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
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Shimono K, Hayashi T, Ikeura Y, Sudo Y, Iwamoto M, Kamo N. Importance of the broad regional interaction for spectral tuning in Natronobacterium pharaonis phoborhodopsin (sensory rhodopsin II). J Biol Chem 2003; 278:23882-9. [PMID: 12690098 DOI: 10.1074/jbc.m301200200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Natronobacterium pharaonis phoborhodopsin (ppR; also called N. pharaonis sensory rhodopsin II, NpsRII) is a photophobic sensor in N. pharaonis, and has a shorter absorption maximum (lambdamax, 500 nm) than those of other archaeal retinal proteins (lambdamax, 560-590 nm) such as bacteriorhodopsin (bR). We constructed chimeric proteins between bR and ppR to investigate the long range interactions effecting the color regulation among archaeal retinal proteins. The lambdamax of B-DEFG/P-ABC was 545 nm, similar to that of bR expressed in Escherichia coli (lambdamax, 550 nm). B-DEFG/P-ABC means a chimera composed of helices D, E, F, and G of bR and helices A, B, and C of ppR. This indicates that the major factor(s) determining the difference in lambdamax between bR and ppR exist in helices DEFG. To specify the more minute regions for the color determination between bR and ppR, we constructed 15 chimeric proteins containing helices D, E, F, and G of bR. According to the absorption spectra of the various chimeric proteins, the interaction between helices D and E as well as the effect of the hydroxyl group around protonated Schiff base on helix G (Thr-204 for ppR and Ala-215 for bR) are the main factors for spectral tuning between bR and ppR.
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Affiliation(s)
- Kazumi Shimono
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.
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Aharoni A, Khatchatouriants A, Manevitch A, Lewis A, Sheves M. Protein−β-Ionone Ring Interactions Enhance the Light-Induced Dipole of the Chromophore in Bacteriorhodopsin. J Phys Chem B 2003. [DOI: 10.1021/jp027702q] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amir Aharoni
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel, and Department of Applied Physics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Artium Khatchatouriants
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel, and Department of Applied Physics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alexandra Manevitch
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel, and Department of Applied Physics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Aaron Lewis
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel, and Department of Applied Physics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Mordechai Sheves
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel, and Department of Applied Physics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Torii H. Vibrational polarization and opsin shift of retinal schiff bases: theoretical study. J Am Chem Soc 2002; 124:9272-7. [PMID: 12149034 DOI: 10.1021/ja017279j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The changes in the electronic excitation energy arising from molecular structural displacement induced by external electric field (so-called vibrational polarization) are examined theoretically for the protonated and neutral 11-cis retinal Schiff bases. It is shown that the magnitude of the field-induced structural displacement is significantly large for the protonated species, so that the change in the electronic excitation energy arising from this structural displacement is of the same order of magnitude as that arising from the direct effect of electric field on the electronic wave function. These two effects contribute additively to the field-induced spectral shift. The intensity-carrying mode (ICM) theory is employed to extract a single vibrational mode (called primary infrared ICM) that is most important for the field-induced structural displacement. A simple one-dimensional model is constructed, and the extent to which we can interpret the field-induced spectral shift by such a model is examined. In the case of the neutral species, only a small change in the electronic excitation energy is induced by external electric field, mainly because the vibrational polarizability of this species is small. The meaning of these results in the spectral tuning of visual pigments is discussed.
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Affiliation(s)
- Hajime Torii
- Department of Chemistry, School of Education, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan.
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Kandori H, Ichioka T, Sasaki M. Photoisomerization of the rhodopsin chromophore in clay interlayers at 77 K. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)00096-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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41
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Shimono K, Ikeura Y, Sudo Y, Iwamoto M, Kamo N. Environment around the chromophore in pharaonis phoborhodopsin: mutation analysis of the retinal binding site. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1515:92-100. [PMID: 11718665 DOI: 10.1016/s0005-2736(01)00394-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Phoborhodopsin (pR or sensory rhodopsin II, sRII) and pharaonis phoborhodopsin (ppR or pharaonis sRII, psRII) have a unique absorption maximum (lambda(max)) compared with three other archaeal rhodopsins: lambda(max) of pR and ppR is approx. 500 nm and of others (e.g. bacteriorhodopsin, bR) is 560-590 nm. To determine the residue contributing to the opsin shift from ppR to bR, we constructed various ppR mutants, in which a single residue was substituted for a residue corresponding to that of bR. The residues mutated were those which differ from that of bR and locate within 5 A from the conjugated polyene chain of the chromophore or any methyl group of the polyene chain. The shifts of lambda(max) of all mutants were small, however. We constructed a mutant in which all residues which differ from those of bR in the retinal binding site were simultaneously substituted for those of bR, but the shift was only from 499 to 509 nm. Next, we constructed a mutant in which 10 residues located within 5 A from the polyene as described above were simultaneously substituted. Only 44% of the opsin shift (lambda(max) of 524 nm) from ppR to bR was obtained even when all amino acids around the chromophore were replaced by the same residues as bR. We therefore conclude that the structural factor is more important in accounting for the difference of lambda(max) between ppR and bR rather than amino acid substitutions. The possible structural factors are discussed.
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Affiliation(s)
- K Shimono
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Hokkaido University, 060-0812, Sapporo, Japan
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Aharoni A, Weiner L, Lewis A, Ottolenghi M, Sheves M. Nonisomerizable non-retinal chromophores initiate light-induced conformational alterations in bacterioopsin. J Am Chem Soc 2001; 123:6612-6. [PMID: 11439048 DOI: 10.1021/ja004035a] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photoactivation of retinal proteins is usually interpreted in terms of C=C photoisomerization of the retinal moiety, which triggers appropriate conformational changes in the protein. In this work several dye molecules, characterized by a completely rigid structure in which no double-bond isomerization is possible, were incorporated into the binding site of bacteriorhodopsin (bR). Using a light-induced chemical reaction of a labeled EPR probe, it was observed that specific conformational alterations in the protein are induced following light absorption by the dye molecules occupying the binding site. The exact nature of these changes and their relationship to those occurring in the bR photocycle are still unclear. Nevertheless, their occurrence proves that C=C or C=NH(+) isomerization is not a prerequisite for protein conformational changes in a retinal protein. More generally, we show that conformational changes, leading to changes in reactivity, may be induced in proteins by optical excitation of simple nonisomerizable dyes located in the macromolecular matrix.
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Affiliation(s)
- A Aharoni
- Department of Organic Chemistry and Department of Chemical Services, The Weizmann Institute of Science, Rehovot 76100, Israel
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Houjou H, Inoue Y, Sakurai M. Study of the Opsin Shift of Bacteriorhodopsin: Insight from QM/MM Calculations with Electronic Polarization Effects of the Protein Environment. J Phys Chem B 2001. [DOI: 10.1021/jp0032863] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hirohiko Houjou
- Department of Biomolecular Engineering, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yoshio Inoue
- Department of Biomolecular Engineering, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Minoru Sakurai
- Department of Biomolecular Engineering, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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Ishiguro M. A Mechanism of Primary Photoactivation Reactions of Rhodopsin: Modeling of the Intermediates in the Rhodopsin Photocycle. J Am Chem Soc 2000. [DOI: 10.1021/ja9921367] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masaji Ishiguro
- Contribution from the Suntory Institute for Bioorganic Research, 1-1 Wakayamadai, Shimamoto, Osaka 618-8503, Japan
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Lin SW, Sakmar TP. Colour tuning mechanisms of visual pigments. NOVARTIS FOUNDATION SYMPOSIUM 1999; 224:124-35; discussion 135-41, 181-90. [PMID: 10614049 DOI: 10.1002/9780470515693.ch8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Spectral tuning by visual pigments involves modulation of physical properties of the 11-cis-retinylidene protonated Schiff base (PSB) chromophore by amino acid side chains in and around the chromophore-binding pocket. Specific molecular contacts between the chromophore and the amino acid side chains of the opsin chromophore-binding pocket have been determined recently using an interdisciplinary approach consisting of site-directed mutagenesis, optical and vibrational spectroscopy, and molecular graphics modelling. These studies provide insight into the mechanism of spectral tuning among visual pigments. In blue pigments a majority of the opsin shift is caused by polar amino acid side chains arrayed about the PSB to increase the energy gap between the ground (S0) and excited states (S1). In addition, a specific tyrosine near the chromophore ring causes a decrease in solvent polarizability. Other amino acid residues alter the binding pocket structure to strengthen electrostatic interaction between the PSB and its counterion and/or solvent dipoles. In the green and red pigments, the work of Kochendoerfer et al (1997; Biochemistry 26:6577-6587) demonstrates that local structural perturbations at the PSB or elsewhere are not responsible for spectral tuning. Instead, the green-to-red opsin shift is best explained by dipolar side chains near the chromophore ring that lower the transition energy that occurs upon electronic excitation by affecting the change in electric dipole moment. In summary, the absorption maximum of a visual pigment is primarily regulated by the interaction of the chromophore charge distribution with dipolar residues in its opsin chromophore-binding pocket. The work presented in this paper is reported in greater detail in Lin et al.
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Affiliation(s)
- S W Lin
- Howard Hughes Medical Institute, Rockefeller University, New York, NY 10021, USA
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Makino CL, Groesbeek M, Lugtenburg J, Baylor DA. Spectral tuning in salamander visual pigments studied with dihydroretinal chromophores. Biophys J 1999; 77:1024-35. [PMID: 10423447 PMCID: PMC1300393 DOI: 10.1016/s0006-3495(99)76953-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
In visual pigments, opsin proteins regulate the spectral absorption of a retinal chromophore by mechanisms that change the energy level of the excited electronic state relative to the ground state. We have studied these mechanisms by using photocurrent recording to measure the spectral sensitivities of individual red rods and red (long-wavelength-sensitive) and blue (short-wavelength-sensitive) cones of salamander before and after replacing the native 3-dehydro 11-cis retinal chromophore with retinal analogs: 11-cis retinal, 3-dehydro 9-cis retinal, 9-cis retinal, and 5,6-dihydro 9-cis retinal. The protonated Schiff's bases of analogs with unsaturated bonds in the ring had broader spectra than the same chromophores bound to opsins. Saturation of the bonds in the ring reduced the spectral bandwidths of the protonated Schiff's bases and the opsin-bound chromophores and made them similar to each other. This indicates that torsion of the ring produces spectral broadening and that torsion is limited by opsin. Saturating the 5,6 double bond in retinal reduced the perturbation of the chromophore by opsin in red and in blue cones but not in red rods. Thus an interaction between opsin and the chromophoric ring shifts the spectral maxima of the red and blue cone pigments, but not that of the red rod pigment.
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Affiliation(s)
- C L Makino
- Department of Ophthalmology, Harvard Medical School, and the Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114, USA.
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Abstract
The absorption maximum of the retinal chromophore in color visual pigments is tuned by interactions with the protein (opsin) to which it is bound. Recent advances in the expression of rhodopsin-like transmembrane receptors and in spectroscopic techniques have allowed us to measure resonance Raman vibrational spectra of the retinal chromophore in recombinant visual pigments to examine the molecular basis of this spectral tuning. The dominant physical mechanism responsible for the opsin shift in color vision is the interaction of dipolar amino acid residues with the ground- and excited-state charge distributions of the chromophore.
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Affiliation(s)
- G G Kochendoerfer
- Dept of Chemistry, University of California, Berkeley, CA 94720, USA
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Lewis A, Khatchatouriants A, Treinin M, Chen Z, Peleg G, Friedman N, Bouevitch O, Rothman Z, Loew L, Sheres M. Second-harmonic generation of biological interfaces: probing the membrane protein bacteriorhodopsin and imaging membrane potential around GFP molecules at specific sites in neuronal cells of C. elegans. Chem Phys 1999. [DOI: 10.1016/s0301-0104(99)00128-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Abstract
Recent studies on rhodopsin structure and function are reviewed and the properties of vertebrate as well as invertebrate rhodopsin described. Open issues such as the 'red shift' of the absorbance spectra are emphasized in the light of the present model of the retinal-binding pocket. The processes that restore the rhodopsin content in photoreceptors are also presented with a comparison between vertebrate and invertebrate visual systems. The central role of rhodopsin in the phototransduction cascade becomes evident by examining the main reports on light-activated conformational changes of rhodopsin and its interaction with transducin. Shut-off mechanisms are considered by reporting the studies on the sites of rhodopsin phosphorylation and arrestin binding. Furthermore, recent findings on the energetics of phototransduction point out that the ATP needed for photoreception in vertebrates is synthesized in the outer segments where phototransduction events take place.
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Affiliation(s)
- I M Pepe
- Institute of Biophysics, Faculty of Medicine, University of Genoa, Italy.
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50
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Lin SW, Kochendoerfer GG, Carroll KS, Wang D, Mathies RA, Sakmar TP. Mechanisms of spectral tuning in blue cone visual pigments. Visible and raman spectroscopy of blue-shifted rhodopsin mutants. J Biol Chem 1998; 273:24583-91. [PMID: 9733753 DOI: 10.1074/jbc.273.38.24583] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Spectral tuning by visual pigments involves the modulation of the physical properties of the chromophore (11-cis-retinal) by amino acid side chains that compose the chromophore-binding pocket. We identified 12 amino acid residues in the human blue cone pigment that might induce the required green-to-blue opsin shift. The simultaneous substitution of nine of these sites in rhodopsin (M86L, G90S, A117G, E122L, A124T, W265Y, A292S, A295S, and A299C) shifted the absorption maximum from 500 to 438 nm, accounting for 2,830 cm-1, or 80%, of the opsin shift between rhodopsin and the blue cone pigment. Raman spectroscopy of mutant pigments shows that the dielectric character and architecture of the chromophore-binding pocket are specifically altered. An increase in the number of dipolar side chains near the protonated Schiff base of retinal increases the ground-excited state energy gap via long range dipole-dipole Coulomb interaction. In addition, the W265Y substitution causes a decrease in solvent polarizability near the chromophore ring structure. Finally, two substitutions on transmembrane helix 3 (A117G and E122L) act in combination with the other substitutions to alter the binding-pocket structure, resulting in stronger interaction of the protonated Schiff base group with the surrounding dipolar groups and the counterion. Taken together, these results identify the amino acid side chains and the underlying physical mechanisms responsible for a majority of the opsin shift in blue visual pigments.
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Affiliation(s)
- S W Lin
- Howard Hughes Medical Institute, Laboratory of Molecular Biology and Biochemistry, The Rockefeller University, New York, New York 10021, USA
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