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Katayama K, Gulati S, Ortega JT, Alexander NS, Sun W, Shenouda MM, Palczewski K, Jastrzebska B. Specificity of the chromophore-binding site in human cone opsins. J Biol Chem 2019; 294:6082-6093. [PMID: 30770468 DOI: 10.1074/jbc.ra119.007587] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/13/2019] [Indexed: 01/21/2023] Open
Abstract
The variable composition of the chromophore-binding pocket in visual receptors is essential for vision. The visual phototransduction starts with the cis-trans isomerization of the retinal chromophore upon absorption of photons. Despite sharing the common 11-cis-retinal chromophore, rod and cone photoreceptors possess distinct photochemical properties. Thus, a detailed molecular characterization of the chromophore-binding pocket of these receptors is critical to understanding the differences in the photochemistry of vision between rods and cones. Unlike for rhodopsin (Rh), the crystal structures of cone opsins remain to be determined. To obtain insights into the specific chromophore-protein interactions that govern spectral tuning in human visual pigments, here we harnessed the unique binding properties of 11-cis-6-membered-ring-retinal (11-cis-6mr-retinal) with human blue, green, and red cone opsins. To unravel the specificity of the chromophore-binding pocket of cone opsins, we applied 11-cis-6mr-retinal analog-binding analyses to human blue, green, and red cone opsins. Our results revealed that among the three cone opsins, only blue cone opsin can accommodate the 11-cis-6mr-retinal in its chromophore-binding pocket, resulting in the formation of a synthetic blue pigment (B6mr) that absorbs visible light. A combination of primary sequence alignment, molecular modeling, and mutagenesis experiments revealed the specific amino acid residue 6.48 (Tyr-262 in blue cone opsins and Trp-281 in green and red cone opsins) as a selectivity filter in human cone opsins. Altogether, the results of our study uncover the molecular basis underlying the binding selectivity of 11-cis-6mr-retinal to the cone opsins.
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Affiliation(s)
- Kota Katayama
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106; Department of Life Science and Applied Chemistry, Showa-ku, Nagoya 466-8555, Japan; OptoBio Technology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Sahil Gulati
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697
| | - Joseph T Ortega
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Nathan S Alexander
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Wenyu Sun
- Polgenix Inc., Cleveland, Ohio 44106
| | - Marina M Shenouda
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697; Polgenix Inc., Cleveland, Ohio 44106.
| | - Beata Jastrzebska
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106.
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Ebrey T. Brighter than the sun: Rajni Govindjee at 80 and her fifty years in photobiology. PHOTOSYNTHESIS RESEARCH 2015; 124:1-5. [PMID: 25739899 DOI: 10.1007/s11120-015-0106-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
We celebrate distinguished photobiologist Rajni Govindjee for her pioneering research in photosynthesis and retinal proteins on the occasion of her 80th birthday.
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Affiliation(s)
- Thomas Ebrey
- University of Washington, Seattle, WA, 98109, USA,
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Nakanishi K, Crouch R. Application of Artificial Pigments to Structure Determination and Study of Photoinduced Transformations of Retinal Proteins. Isr J Chem 2013. [DOI: 10.1002/ijch.199500030] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Kono M, Crouch RK. Probing human red cone opsin activity with retinal analogues. JOURNAL OF NATURAL PRODUCTS 2011; 74:391-394. [PMID: 21314100 PMCID: PMC3064742 DOI: 10.1021/np100749j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Retinal analogues have been used to probe the chromophore binding pocket and function of the rod visual pigment rhodopsin. Despite the high homology between rod and cone visual pigment proteins, conclusions drawn from rhodopsin studies should not necessarily be extrapolated to cone visual pigment proteins. In this study, the effects of full-length and truncated retinal analogues on the human red cone opsin's ability to activate transducin, the G protein in visual transduction, were assessed. The result with beta-ionone (6) confirms that a covalent bond is not necessary to deactivate the red cone opsin. In addition, several small compounds were found able to deactivate this opsin. However, as the polyene chain is extended in a trans configuration beyond the 9-carbon position, the analogues became agonists up to all-trans-retinal (3). The 22-carbon analogue (2) appeared to be neither an agonist nor an inverse agonist. Although the all-trans-C17 (5) analogue was an agonist, the 9-cis-C17 (11) compound was an inverse agonist, a result that differs from that with rhodopsin. These results suggest that the red cone opsin has a more open structure in the chromophore binding region than rhodopsin and its activation or deactivation as a G-protein receptor may be less selective than rhodopsin.
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Affiliation(s)
- Masahiro Kono
- Department of Ophthalmology, Medical University of South Carolina, Charleston, South Carolina 29425, United States.
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van der Steen R, Biesheuvel PL, Lugtenburg J, Erkelens C, Mathies RA. 8,16- And 8,18-methanobacteriorhodopsin. Synthesis and spectroscopy of 8,16- and 8,18-methanoretinal and their interaction with bacterioopsin. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19891080302] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Waddell WH, Dawson PM, Hopkins DL, Rach KL, Uemura M, West JL. Quantitative Analysis of Photochemical Reactions Utilizing High Pressure Liquid Chromatography: Linear Polyenes Related to Vitamin A. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/01483917908060131] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Spooner PJR, Sharples JM, Verhoeven MA, Lugtenburg J, Glaubitz C, Watts A. Relative orientation between the beta-ionone ring and the polyene chain for the chromophore of rhodopsin in native membranes. Biochemistry 2002; 41:7549-55. [PMID: 12056885 DOI: 10.1021/bi020007o] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rotational resonance solid state nuclear magnetic resonance has been used to determine the relative orientation of the beta-ionone ring and the polyene chain of the chromophore 11-Z-retinylidene of rhodopsin in rod outer segment membranes from bovine retina. The bleached protein was regenerated with either 11-Z-[8,18-(13)C(2)]retinal or 11-Z-[8,16/17(13)C(2)]retinal, the latter having only one (13)C label at either of the chemically equivalent positions 16 and 17. Observation of (13)C selectively enriched in the ring methyl groups, C16/17, revealed alternative conformational states for the ring. Minor spectral components comprised around 26% of the chromophore. The major conformation (approximately 74%) has the chemical shift resolution required for measuring internuclear distances to (13)C in the retinal chain (C8) separately from each of these methyl groups. The resulting distance constraints, C8 to C16 and C17 (4.05 +/- 0.25 A) and from C8 to C18 (2.95 +/- 0.15 A), show that the major portion of retinylidene in rhodopsin has a twisted 6-s-cis conformation. The more precise distance measurement made here between C8 and C18 (2.95 A) predicts that the chain is twisted out-of-plane with respect to the ring by a modest amount (C5-C6-C7-C8 torsion angle = -28 +/- 7 degrees ).
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Affiliation(s)
- Paul J R Spooner
- The Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
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Fujimoto Y, Xie R, Tully SE, Berova N, Nakanishi K. Synthesis of 11-cis-locked bicyclo[5.1.0]octanyl retinal and an enantioselective binding to bovine opsin. Chirality 2002; 14:340-6. [PMID: 11968076 DOI: 10.1002/chir.10076] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Both enantiomers of 13-(E) and 13-(Z) isomers of 11-cis-locked bicyclo[5.1.0]octanyl retinal were prepared by an improved synthesis and incubated with bovine opsin. The synthesis also establishes the absolute configuration of the enantiomers. Only one of the enantiomers binds to opsin, thus showing the steric restrictions regarding the middle polyene moiety of the retinoid molecule; this is in sharp contrast to the known leniency of the ring moiety binding site of retinoids. However, although one enantiomer is incorporated into the pigment, the circular dichroic spectrum of the pigment incorporating the bound enantiomer yields only a very weak Cotton effect, showing that, once incorporated, the bicyclo[5.1.0]octanyl chromophore is flattened by the opsin binding site. The titled retinoid was synthesized for study of the absolute conformation of the retinal pigment in rhodopsin.
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Affiliation(s)
- Yukari Fujimoto
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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Lou J, Hashimoto M, Berova N, Nakanishi K. Enantioselective binding of an 11-cis-locked cyclopropyl retinal. The conformation of retinal in bovine rhodopsin. Org Lett 1999; 1:51-4. [PMID: 10822532 DOI: 10.1021/ol990048l] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[formula: see text] The conformation of the retinal chromophore in rhodopsin is central for understanding the visual transduction process. The absolute twist around the 12-s bond of the chromophore in rhodopsin has been determined by studies with 11-cis-locked 11,12-cyclopropylretinal analogues (11S,12R)-2 and (11R,12S)-3, enantioselectively synthesized with the aid of an enzyme. The finding that enantiomer 2 binds to opsin while the other 3 does not defines the absolute sense of twist around the 12-s bond.
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Affiliation(s)
- J Lou
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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Derguini F, Bigge CF, Croteau AA, Balogh-Nair V, Nakanishi K. Visual pigments and bacteriorhodopsins formed from aromatic retinal analogs. Photochem Photobiol 1984; 39:661-5. [PMID: 6739558 DOI: 10.1111/j.1751-1097.1984.tb03906.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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11
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Robert LS, Matsumoto H, Kini A, Asato AE, Denny M, Kropf A, DeGrip WJ. Seven new hindered isomeric rhodopsins. Tetrahedron 1984. [DOI: 10.1016/0040-4020(84)85052-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Towner P, Gaertner W, Walckhoff B, Oesterhelt D, Hopf H. Regeneration of rhodopsin and bacteriorhodopsin. The role of retinal analogues as inhibitors. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 117:353-9. [PMID: 6456145 DOI: 10.1111/j.1432-1033.1981.tb06345.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The rate of regeneration of rhodopsin, from 11-cis-retinal and opsin, and bacteriorhodopsin from all-trans-retinal and bacterio-opsin, in the presence or absence of compounds whose structures partially resemble retinal were measured. Some of these compounds severely slowed down the regeneration process, but did not influence the extent of regeneration. In the case of compounds with a carbonyl functional group they were not joined to the active site of the apo-protein via a Schiff's base linkage since after treatment with NaBH4 an active apo-protein remained. The most effective inhibitors of rhodopsin regeneration were molecules whose structure could be superimposed on 9-cis or 11-cis retinal up to carbon atom 11. These C13 and C15 molecules were not distinguished between aldehyde, ketone or alcohol functional groups. The regeneration of bacteriorhodopsin was not inhibited by retinal analogues with short side chains. The most effective inhibitors were the all-trans C17-aldehyde (beta-ionylideneacetaldehyde) or C18-ketone (beta-ionylidenepent-3-ene-2-one) which, compared to retinal, lack two or three carbon atoms from the end of the poylene chain. The inhibition was very dependent upon the presence of the all-trans isomer and required aldehyde or ketone as functional group nitriles and alcohols were less effective. However, similarly to retinol, the all-trans C17 and C18 alcohols underwent a bathochromic shift and showed fine-structured spectra when mixed with bacterio-opsin.
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Crouch R, Katz S, Nakanishi K, Gawinowicz MA, Balogh-Nair V. Incorporation of 11,12-dihydroretinal into the retinae of vitamin a deprived rats. Photochem Photobiol 1981; 33:91-5. [PMID: 7243905 DOI: 10.1111/j.1751-1097.1981.tb04302.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Groenendijk GW, De Grip WJ, Daemen FJ. Quantitative determination of retinals with complete retention of their geometric configuration. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 617:430-8. [PMID: 7378129 DOI: 10.1016/0005-2760(80)90009-0] [Citation(s) in RCA: 130] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A method is described for the quantitative extraction of retinal in its original isomeric configuration from retinal-containing pigments. Using excess of hydroxylamine under denaturing conditions, the chromophore of retinal bearing natural products is converted into the corresponding retinaloxime with complete retention of geometric configuration. The retinaloximes can be quantitatively extracted with dichloromethane and analyzed by high-performance liquid chromatography.
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Groenendijk GW, Jansen PA, Bonting SL, Daemen FJ. Analysis of geometrically isomeric vitamin A compounds. Methods Enzymol 1980; 67:203-20. [PMID: 7366429 DOI: 10.1016/s0076-6879(80)67029-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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17
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Matsumoto H, Asato AE, Liu RS. 7-cis-porphyropsin from 7-cis-3-dehydroretinal and cattle opsin. Photochem Photobiol 1979; 29:695-8. [PMID: 451009 DOI: 10.1111/j.1751-1097.1979.tb07751.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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18
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Fritz HJ, Belagaje R, Brown EL, Fritz RH, Jones RA, Lees RG, Khorana HG. High-pressure liquid chromatography in polynucleotide synthesis. Biochemistry 1978; 17:1257-67. [PMID: 656387 DOI: 10.1021/bi00600a020] [Citation(s) in RCA: 164] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Reverse phase high-pressure liquid chromatography (HPLC) using columns containing microparticulate materials with bonded octadecyl groups has been developed as a rapid and efficient method for the separation of nucleosides, nucleotides, and, in particular, of protected oligonucleotides which are standard intermediates in the stepwise synthesis of deoxyribopolynucleotides. Reported are extensive studies of the influence of the different purine and pyrimidine bases, of protecting groups, of the phosphate groups, and of the chain lengths of oligonucleotides on their retention on such columns. Further, the application of HPLC in the stepwise synthesis of an oligonucleotide, d(G-G-A-A-G-C-T-T-A-A-C), has been described. The methods, which are herein described, lend themselves to separations on a preparative scale and effect a marked reduction (up to 50%) in the time required for the synthesis of oligonucleotides.
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Tanis SP, Brown RH, Nakanishi K. A convenient synthesis of stereochemically pure retinoids. The synthesis of 10,14-dimethyl retinals. Tetrahedron Lett 1978. [DOI: 10.1016/s0040-4039(01)91422-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Pilkiewicz FG, Pettei MJ, Yudd AP, Nakanishi K. A simple and non-isomerizing procedure for the identification of protein-linked retinals. Exp Eye Res 1977; 24:421-3. [PMID: 858324 DOI: 10.1016/0014-4835(77)90157-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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22
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Mathies R, Freedman TB, Stryer L. Resonance Raman studies of the conformation of retinal in rhodopsin and isorhodopsin. J Mol Biol 1977; 109:367-72. [PMID: 839546 DOI: 10.1016/s0022-2836(77)80040-5] [Citation(s) in RCA: 85] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Pettei MJ, Pilkiewicz FG, Nakanishi K. Preparative liquid chromatography applied to difficult separations. Tetrahedron Lett 1977. [DOI: 10.1016/s0040-4039(01)83686-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Dickerson H, Ferber S, Richardson FS. Molecular orbital calculations on the optical rotatory properties of chiral allene systems. ACTA ACUST UNITED AC 1976. [DOI: 10.1007/bf00548475] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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