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Mizuno M, Sato K, Yamashita T, Sakai K, Imamoto Y, Yamano Y, Wada A, Ohuchi H, Shichida Y, Mizutani Y. Chromophore Structure in an Inactive State of a Novel Photosensor Protein Opn5L1: Resonance Raman Evidence for the Formation of a Deprotonated Adduct at the 11th Carbon Atom. J Phys Chem B 2023; 127:2169-2176. [PMID: 36857774 DOI: 10.1021/acs.jpcb.2c08780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Opsins are photosensitive G protein-coupled receptor proteins and are classified into visual and nonvisual receptors. Opn5L1 is a nonvisual opsin that binds all-trans retinal as a chromophore. A unique feature of Opn5L1 is that the protein exhibits a photocyclic reaction upon photoexcitation. Determining the chromophore structures of intermediates in the photocycle is essential for understanding the functional mechanism of Opn5L1. A previous study revealed that a long-lived intermediate in the photocycle cannot activate the G protein and forms a covalent bond between the retinal chromophore and a nearby cysteine residue. However, the position of this covalent bond in the chromophore remains undetermined. Here, we report a resonance Raman study on isotopically labeled samples in combination with density functional theory calculations and reveal that the 11th carbon atom of the chromophore of the intermediate forms a covalent linkage to the cysteine residue. Furthermore, vibrational assignments based on the isotopic substitutions and density functional theory calculations suggested that the Schiff base of the intermediate is deprotonated. The chromophore structure determined in the present study well explains the mechanism of the photocyclic reaction, which is crucial to the photobiological function of Opn5L1.
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Affiliation(s)
- Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Keita Sato
- Department of Cytology and Histology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama, Okayama 700-8558, Japan
| | - Takahiro Yamashita
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kazumi Sakai
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yasushi Imamoto
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yumiko Yamano
- Comprehensive Education and Research Center, Kobe Pharmaceutical University, Kobe 658-8558, Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-cho, Higashinada, Kobe, Hyogo 658-8558, Japan
| | - Hideyo Ohuchi
- Department of Cytology and Histology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama, Okayama 700-8558, Japan
| | - Yoshinori Shichida
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.,Research Organization for Science and Technology, Ritsumeikan University, Shiga 525-8577, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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Abstract
"Retinoid" is the general term for vitamin A derivatives and chemical compounds that act like vitamin A. Vitamin A are composed of four isoprene units and are named according to their terminal functional group, such as retinol (OH, 1), retinal (CHO, 2), and retinoic acid (CO2H, 3). Vitamin A usually refers to retinol. In the past few decades, major advances in research on vitamin A have improved our understanding of its fundamental roles and physiological significance in living cells. In this review, three types of chemical biology studies using vitamin A analogs are described: (1) conformational studies of the chromophore in retinal proteins (rhodopsin, phoborhodopsin, and retinochrome), especially the conformation around the cyclohexene ring; (2) structure-activity relationship studies of retinoic acid analogs to create new signaling molecules for activating nuclear receptors; and (3) development of a new channelrhodopsin with an absorption maximum at longer wavelength to overcome the various demerits of channelrhodopsins used in optogenetics, as well as the stereoselective synthesis of retinoid isomers and their analogs using a diene-tricarbonyliron complex or a palladium-catalyzed cross-coupling reaction between vinyl triflates and stannyl olefins.
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Álvarez R, Vaz B, Gronemeyer H, de Lera ÁR. Functions, therapeutic applications, and synthesis of retinoids and carotenoids. Chem Rev 2013; 114:1-125. [PMID: 24266866 DOI: 10.1021/cr400126u] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rosana Álvarez
- Departamento de Química Orgánica, Centro de Investigación Biomédica (CINBIO), and Instituto de Investigación Biomédica de Vigo (IBIV), Universidade de Vigo , 36310 Vigo, Spain
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Rossi R, Bellina F, Lessi M, Manzini C. Development and applications of highly selective palladium-catalyzed monocoupling reactions of (cyclo)alkenes and 1,3-alkadienes bearing two or three electrophilic sites and bis(enol triflates) with terminal alkynes. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Cross-Coupling Reactions of Organosilicon Compounds in the Stereocontrolled Synthesis of Retinoids. Chemistry 2012; 18:4401-10. [DOI: 10.1002/chem.201103360] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Indexed: 11/07/2022]
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7
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McLean NJ, Gansmuller A, Concistre M, Brown LJ, Levitt MH, Brown RC. Syntheses of 13C2-labelled 11Z-retinals. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.07.092] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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8
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Okitsu T, Nakazawa D, Nakagawa K, Okano T, Wada A. Synthesis and Biological Evaluation of 9Z-Retinoic Acid Analogs Having 2-Substituted Benzo[b]furan. Chem Pharm Bull (Tokyo) 2010; 58:418-22. [DOI: 10.1248/cpb.58.418] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Takashi Okitsu
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University
| | - Daisuke Nakazawa
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University
| | - Kimie Nakagawa
- Department of Hygienic Sciences, Kobe Pharmaceutical University
| | - Toshio Okano
- Department of Hygienic Sciences, Kobe Pharmaceutical University
| | - Akimori Wada
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University
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Donaldson WA, Chaudhury S. Recent Applications of Acyclic (Diene)iron Complexes and (Dienyl)iron Cations in Organic Synthesis. European J Org Chem 2009; 2009:3831-3843. [PMID: 21709767 DOI: 10.1002/ejoc.200900141] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Complexation of (tricarbonyl)iron to an acyclic diene serves to protect the ligand against oxidation, reduction and cycloaddition reactions while the steric bulk of this adjunct serves to direct the approach reagents to unsaturated groups attached to the diene onto the face opposite to iron. Furthermore, the Fe(CO)(3) moiety can serve to stabilize carbocation centers adjacent to the diene (i.e. pentadienyl-iron cations). Recent applications of these reactivities to the synthesis of polyene, cyclopropane, cycloheptadiene and cyclohexenone containing natural products or analogs will be presented.
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Affiliation(s)
- William A Donaldson
- Department of Chemistry, Marquette University, P. O. Box 1881, Milwaukee, WI 53201-1881 USA
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Brown MF, Martínez-Mayorga K, Nakanishi K, Salgado GFJ, Struts AV. Retinal conformation and dynamics in activation of rhodopsin illuminated by solid-state H NMR spectroscopy. Photochem Photobiol 2009; 85:442-53. [PMID: 19267870 DOI: 10.1111/j.1751-1097.2008.00510.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Solid-state NMR spectroscopy gives a powerful avenue for investigating G protein-coupled receptors and other integral membrane proteins in a native-like environment. This article reviews the use of solid-state (2)H NMR to study the retinal cofactor of rhodopsin in the dark state as well as the meta I and meta II photointermediates. Site-specific (2)H NMR labels have been introduced into three regions (methyl groups) of retinal that are crucially important for the photochemical function of rhodopsin. Despite its phenomenal stability (2)H NMR spectroscopy indicates retinal undergoes rapid fluctuations within the protein binding cavity. The spectral lineshapes reveal the methyl groups spin rapidly about their three-fold (C(3)) axes with an order parameter for the off-axial motion of SC(3) approximately 0.9. For the dark state, the (2)H NMR structure of 11-cis-retinal manifests torsional twisting of both the polyene chain and the beta-ionone ring due to steric interactions of the ligand and the protein. Retinal is accommodated within the rhodopsin binding pocket with a negative pretwist about the C11=C12 double bond. Conformational distortion explains its rapid photochemistry and reveals the trajectory of the 11-cis to trans isomerization. In addition, (2)H NMR has been applied to study the retinylidene dynamics in the dark and light-activated states. Upon isomerization there are drastic changes in the mobility of all three methyl groups. The relaxation data support an activation mechanism whereby the beta-ionone ring of retinal stays in nearly the same environment, without a large displacement of the ligand. Interactions of the beta-ionone ring and the retinylidene Schiff base with the protein transmit the force of the retinal isomerization. Solid-state (2)H NMR thus provides information about the flow of energy that triggers changes in hydrogen-bonding networks and helix movements in the activation mechanism of the photoreceptor.
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Affiliation(s)
- Michael F Brown
- Department of Chemistry, University of Arizona, Tucson, AZ, USA.
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11
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12
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Preparation and biological evaluation of 5-substituted retinoic acids. Bioorg Med Chem 2008; 16:8471-81. [PMID: 18760926 DOI: 10.1016/j.bmc.2008.08.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 08/07/2008] [Accepted: 08/08/2008] [Indexed: 11/23/2022]
Abstract
Various 5-substituted retinoic acids were prepared by a palladium-catalyzed cross coupling reactions of vinyl nonaflates and E- or Z-3-tributylstannyl-2-beten-1-ol as a key reaction. These coupling products were then converted to the corresponding all-E- and 9Z-retinoic acid analogs via Horner-Emmons reaction and subsequent basic hydrolysis, and their biological activities were evaluated. The all-E-derivatives, 5-butyl and isobutyl analogs exhibited stronger effects for anti-proliferative and differentiation-inducing activities in HL-60 cells. In contrast, in 9Z-derivatives, none of the analogs showed any activity.
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Wada A, Wang F, Ito M. A Convenient and Stereoselective Synthesis of 11Z-3,4-Didehydroretinal by Horner-Emmons Reaction Using Diphenyl Phosphonate. Chem Pharm Bull (Tokyo) 2008; 56:112-4. [DOI: 10.1248/cpb.56.112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Akimori Wada
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University
| | - Fei Wang
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University
| | - Masayoshi Ito
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University
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Brown MF, Heyn MP, Job C, Kim S, Moltke S, Nakanishi K, Nevzorov AA, Struts AV, Salgado GFJ, Wallat I. Solid-state 2H NMR spectroscopy of retinal proteins in aligned membranes. BIOCHIMICA ET BIOPHYSICA ACTA 2007; 1768:2979-3000. [PMID: 18021739 PMCID: PMC5233718 DOI: 10.1016/j.bbamem.2007.10.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 10/10/2007] [Accepted: 10/10/2007] [Indexed: 11/21/2022]
Abstract
Solid-state 2H NMR spectroscopy gives a powerful avenue to investigating the structures of ligands and cofactors bound to integral membrane proteins. For bacteriorhodopsin (bR) and rhodopsin, retinal was site-specifically labeled by deuteration of the methyl groups followed by regeneration of the apoprotein. 2H NMR studies of aligned membrane samples were conducted under conditions where rotational and translational diffusion of the protein were absent on the NMR time scale. The theoretical lineshape treatment involved a static axial distribution of rotating C-C2H3 groups about the local membrane frame, together with the static axial distribution of the local normal relative to the average normal. Simulation of solid-state 2H NMR lineshapes gave both the methyl group orientations and the alignment disorder (mosaic spread) of the membrane stack. The methyl bond orientations provided the angular restraints for structural analysis. In the case of bR the retinal chromophore is nearly planar in the dark- and all-trans light-adapted states, as well upon isomerization to 13-cis in the M state. The C13-methyl group at the "business end" of the chromophore changes its orientation to the membrane upon photon absorption, moving towards W182 and thus driving the proton pump in energy conservation. Moreover, rhodopsin was studied as a prototype for G protein-coupled receptors (GPCRs) implicated in many biological responses in humans. In contrast to bR, the retinal chromophore of rhodopsin has an 11-cis conformation and is highly twisted in the dark state. Three sites of interaction affect the torsional deformation of retinal, viz. the protonated Schiff base with its carboxylate counterion; the C9-methyl group of the polyene; and the beta-ionone ring within its hydrophobic pocket. For rhodopsin, the strain energy and dynamics of retinal as established by 2H NMR are implicated in substituent control of activation. Retinal is locked in a conformation that is twisted in the direction of the photoisomerization, which explains the dark stability of rhodopsin and allows for ultra-fast isomerization upon absorption of a photon. Torsional strain is relaxed in the meta I state that precedes subsequent receptor activation. Comparison of the two retinal proteins using solid-state 2H NMR is thus illuminating in terms of their different biological functions.
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Affiliation(s)
- Michael F Brown
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA.
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Tanaka K, Struts AV, Krane S, Fujioka N, Salgado GFJ, Martínez-Mayorga K, Brown MF, Nakanishi K. Synthesis of CD3-Labeled 11-cis-Retinals and Application to Solid-State Deuterium NMR Spectroscopy of Rhodopsin. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.2177] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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López S, Montenegro J, Saá C. Highly Convergent, Stereospecific Synthesis of 11-cis-Retinoids by Metal-Catalyzed Cross-Coupling Reactions of (Z)-1-Alkenylmetals. J Org Chem 2007; 72:9572-81. [DOI: 10.1021/jo701664r] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Susana López
- Departamento de Química Orgánica, Facultade de Química, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Javier Montenegro
- Departamento de Química Orgánica, Facultade de Química, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Carlos Saá
- Departamento de Química Orgánica, Facultade de Química, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Luo J, Cheng YJ, Kim TD, Hau S, Jang SH, Shi Z, Zhou XH, Jen AKY. Facile Synthesis of Highly Efficient Phenyltetraene-Based Nonlinear Optical Chromophores for Electrooptics. Org Lett 2006; 8:1387-90. [PMID: 16562898 DOI: 10.1021/ol060178b] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] A facile synthetic route has been developed to convert an electron-rich, sterically hindered dialkylaminodienone into a conjugated dialkylaminotrienal with good yield. The derived dialkylaminotetraene-type nonlinear optical chromophores possess an all-trans conformation and can be functionalized with fluoro-dendron to provide proper shape modification for poling. Polymers doped with two examples of these chromophores in high concentrations have been poled to afford ultra-large electrooptic coefficients (r(33)) of 208 and 262 pm/V, respectively, at the measuring wavelength of 1.31 mum.
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Affiliation(s)
- Jingdong Luo
- Department of Materials Science & Engineering and Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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Hirano T, Fujioka N, Imai H, Kandori H, Wada A, Ito M, Shichida Y. Assignment of the Vibrational Modes of the Chromophores of Iodopsin and Bathoiodopsin: Low-Temperature Fourier Transform Infrared Spectroscopy of 13C- and 2H-Labeled Iodopsins. Biochemistry 2006; 45:1285-94. [PMID: 16430225 DOI: 10.1021/bi0517077] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To investigate the chromophore structures of iodopsin and its low-temperature photoproducts, we have assigned their vibrational bands in the Fourier transform infrared (FTIR) spectra using iodopsin samples that were reconstituted with a series of (13)C- and deuterium-labeled retinals. The analyses of the vibrational bands in the fingerprint and hydrogen-out-of-plane (HOOP) regions indicated that the structure of the chromophores in the iodopsin system differs near their centers from those in the rhodopsin system. Compared to rhodopsin, the chromophore of the batho intermediate of iodopsin is twisted in the C(12) to C(14) regions but is more planar around C(11) region. The large amount of twisting was reduced by removing the chloride ion from the iodopsin, suggesting that this twisting hinders the relaxation of the torsion near C(11) necessary for the transition to the lumi intermediate and thus results in the thermal reversion of the batho intermediate back to the iodopsin. From the analyses of the C=NH and C=ND stretching bands, we conclude that the displacement of the Schiff base region upon photoisomerization of the chromophore is restricted, as is the case for rhodopsin. These results indicated that iodopsin's chromophore has a unique structure near its center and that this difference is enhanced by the binding of chloride nearby.
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Affiliation(s)
- Takahiro Hirano
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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Wada A, Fukunaga K, Ito M, Mizuguchi Y, Nakagawa K, Okano T. Preparation and biological activity of 13-substituted retinoic acids. Bioorg Med Chem 2004; 12:3931-42. [PMID: 15210160 DOI: 10.1016/j.bmc.2004.04.047] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Revised: 04/28/2004] [Accepted: 04/28/2004] [Indexed: 11/19/2022]
Abstract
13-Demethyl or 13-substituted all-E- and 9Z-retinoic acids were synthesized using a palladium-catalyzed coupling reaction of enol triflates and tributylstannylolefins. Their biological activities were then measured. The 13-ethyl analogs exhibited approximately one-half of the antiproliferative and differentiation-inducing activity of ATRA in HL-60 cells. In contrast, in the 9Z-derivatives, all analogs, except for the 13-butyl derivatives, showed apoptosis-inducing activity.
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Affiliation(s)
- Akimori Wada
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University, 4-19-1, Motoyamakita-machi, Higashinada, Kobe 658-8558, Japan.
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