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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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2
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Hernández-Rodríguez EW, Escorcia AM, van der Kamp MW, Montero-Alejo AL, Caballero J. Multi-scale simulation reveals that an amino acid substitution increases photosensitizing reaction inputs in Rhodopsins. J Comput Chem 2020; 41:2278-2295. [PMID: 32757375 DOI: 10.1002/jcc.26392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 06/27/2020] [Accepted: 07/04/2020] [Indexed: 11/11/2022]
Abstract
Evaluating the availability of molecular oxygen (O2 ) and energy of excited states in the retinal binding site of rhodopsin is a crucial challenging first step to understand photosensitizing reactions in wild-type (WT) and mutant rhodopsins by absorbing visible light. In the present work, energies of the ground and excited states related to 11-cis-retinal and the O2 accessibility to the β-ionone ring are evaluated inside WT and human M207R mutant rhodopsins. Putative O2 pathways within rhodopsins are identified by using molecular dynamics simulations, Voronoi-diagram analysis, and implicit ligand sampling while retinal energetic properties are investigated through density functional theory, and quantum mechanical/molecular mechanical methods. Here, the predictions reveal that an amino acid substitution can lead to enough energy and O2 accessibility in the core hosting retinal of mutant rhodopsins to favor the photosensitized singlet oxygen generation, which can be useful in understanding retinal degeneration mechanisms and in designing blue-lighting-absorbing proteic photosensitizers.
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Affiliation(s)
- Erix W Hernández-Rodríguez
- Laboratorio de Bioinformática y Química Computacional, Escuela de Química y Farmacia, Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
| | - Andrés M Escorcia
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
| | | | - Ana L Montero-Alejo
- Departamento de Física, Facultad de Ciencias Naturales, Matemática y del Medio Ambiente (FCNMM), Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Julio Caballero
- Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
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3
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Xie P, Zhou P, Alsaedi A, Zhang Y. pH-dependent absorption spectra of rhodopsin mutant E113Q: On the role of counterions and protein. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 174:25-31. [PMID: 27865136 DOI: 10.1016/j.saa.2016.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/08/2016] [Accepted: 11/12/2016] [Indexed: 06/06/2023]
Abstract
The absorption spectra of bovine rhodopsin mutant E113Q in solutions were investigated at the molecular level by using a hybrid quantum mechanics/molecular mechanics (QM/MM) method. The calculations suggest the mechanism of the absorption variations of E113Q at different pH values. The results indicate that the polarizations of the counterions in the vicinity of Schiff base under protonation and unprotonation states of the mutant E113Q would be a crucial factor to change the energy gap of the retinal to tune the absorption spectra. Glu-181 residue, which is close to the chromophore, cannot serve as the counterion of the protonated Schiff base of E113Q in dark state. Moreover, the results of the absorption maximum in mutant E113Q with the various anions (Cl-, Br-, I- and NO3-) manifested that the mutant E113Q could have the potential for use as a template of anion biosensors at visible wavelength.
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Affiliation(s)
- Peng Xie
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Ahmed Alsaedi
- Nonlinear Analysis and Applied Mathematics (NAAM) Research Group, Department of Mathematics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Yan Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China.
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4
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Sandberg MN, Greco JA, Wagner NL, Amora TL, Ramos LA, Chen MH, Knox BE, Birge RR. Low-Temperature Trapping of Photointermediates of the Rhodopsin E181Q Mutant. SOJ BIOCHEMISTRY 2015; 1. [PMID: 25621306 DOI: 10.15226/2376-4589/1/1/00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Three active-site components in rhodopsin play a key role in the stability and function of the protein: 1) the counter-ion residues which stabilize the protonated Schiff base, 2) water molecules, and 3) the hydrogen-bonding network. The ionizable residue Glu-181, which is involved in an extended hydrogen-bonding network with Ser-186, Tyr-268, Tyr-192, and key water molecules within the active site of rhodopsin, has been shown to be involved in a complex counter-ion switch mechanism with Glu-113 during the photobleaching sequence of the protein. Herein, we examine the photobleaching sequence of the E181Q rhodopsin mutant by using cryogenic UV-visible spectroscopy to further elucidate the role of Glu-181 during photoactivation of the protein. We find that lower temperatures are required to trap the early photostationary states of the E181Q mutant compared to native rhodopsin. Additionally, a Blue Shifted Intermediate (BSI, λmax = 498 nm, 100 K) is observed after the formation of E181Q Bathorhodopsin (Batho, λmax = 556 nm, 10 K) but prior to formation of E181Q Lumirhodopsin (Lumi, λmax = 506 nm, 220 K). A potential energy diagram of the observed photointermediates suggests the E181Q Batho intermediate has an enthalpy value 7.99 KJ/mol higher than E181Q BSI, whereas in rhodopsin, the BSI is 10.02 KJ/mol higher in enthalpy than Batho. Thus, the Batho to BSI transition is enthalpically driven in E181Q and entropically driven in native rhodopsin. We conclude that the substitution of Glu-181 with Gln-181 results in a significant perturbation of the hydrogen-bonding network within the active site of rhodopsin. In addition, the removal of a key electrostatic interaction between the chromophore and the protein destabilizes the protein in both the dark state and Batho intermediate conformations while having a stabilizing effect on the BSI conformation. The observed destabilization upon this substitution further supports that Glu-181 is negatively charged in the early intermediates of the photobleaching sequence of rhodopsin.
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Affiliation(s)
- Megan N Sandberg
- Departments of Chemistry and Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Jordan A Greco
- Departments of Chemistry and Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Nicole L Wagner
- Departments of Chemistry and Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Tabitha L Amora
- Departments of Chemistry and Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Lavoisier A Ramos
- Departments of Chemistry and Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Min-Hsuan Chen
- Departments of Biochemistry and Molecular Biology and Ophthalmology State University of New York Upstate Medical University, Syracuse, NY 13210, USA
| | - Barry E Knox
- Departments of Biochemistry and Molecular Biology and Ophthalmology State University of New York Upstate Medical University, Syracuse, NY 13210, USA
| | - Robert R Birge
- Departments of Chemistry and Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
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5
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Walczak E, Andruniów T. Impacts of retinal polyene (de)methylation on the photoisomerization mechanism and photon energy storage of rhodopsin. Phys Chem Chem Phys 2015; 17:17169-81. [DOI: 10.1039/c5cp01939g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Similar to native rhodopsin, a two-mode space-saving isomerization mechanism drives the photoreaction in (de)methylated rhodopsin analogues.
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Affiliation(s)
- Elżbieta Walczak
- Department of Chemistry
- Wroclaw University of Technology
- 50-370 Wroclaw
- Poland
| | - Tadeusz Andruniów
- Department of Chemistry
- Wroclaw University of Technology
- 50-370 Wroclaw
- Poland
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7
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Hernández-Rodríguez EW, Sánchez-García E, Crespo-Otero R, Montero-Alejo AL, Montero LA, Thiel W. Understanding Rhodopsin Mutations Linked to the Retinitis pigmentosa Disease: a QM/MM and DFT/MRCI Study. J Phys Chem B 2012; 116:1060-76. [DOI: 10.1021/jp2037334] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Erix Wiliam Hernández-Rodríguez
- Departamento de Bioquímica, Instituto de Ciencias Básicas y Preclínicas “Victoria de Girón”, 11600 Havana City, Cuba, and Charité Centrum für Innere Medizin und Dermatologie, Biomedizinisches Forschungszentrum, Campus Virchow, Charité-Universitätsmedizin, 13353 Berlin, Germany
| | | | | | - Ana Lilian Montero-Alejo
- Laboratorio de Química Computacional y Teórica, Departamento de Química Física, Universidad de La Habana, 10400 Havana City, Cuba
| | - Luis Alberto Montero
- Laboratorio de Química Computacional y Teórica, Departamento de Química Física, Universidad de La Habana, 10400 Havana City, Cuba
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, 45470 Germany
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8
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Sandberg MN, Amora TL, Ramos LS, Chen MH, Knox BE, Birge RR. Glutamic acid 181 is negatively charged in the bathorhodopsin photointermediate of visual rhodopsin. J Am Chem Soc 2011; 133:2808-11. [PMID: 21319741 DOI: 10.1021/ja1094183] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Assignment of the protonation state of the residue Glu-181 is important to our understanding of the primary event, activation processes and wavelength selection in rhodopsin. Despite extensive study, there is no general agreement on the protonation state of this residue in the literature. Electronic assignment is complicated by the location of Glu-181 near the nodal point in the electrostatic charge shift that accompanies excitation of the chromophore into the low-lying, strongly allowed ππ* state. Thus, the charge on this residue is effectively hidden from electronic spectroscopy. This situation is resolved in bathorhodopsin, because photoisomerization of the chromophore places Glu-181 well within the region of negative charge shift following excitation. We demonstrate that Glu-181 is negatively charged in bathorhodopsin on the basis of the shift in the batho absorption maxima at 10 K [λ(max) band (native) = 544 ± 2 nm, λ(max) band (E181Q) = 556 ± 3 nm] and the decrease in the λ(max) band oscillator strength (0.069 ± 0.004) of E181Q relative to that of the native protein. Because the primary event in rhodopsin does not include a proton translocation or disruption of the hydrogen-bonding network within the binding pocket, we may conclude that the Glu-181 residue in rhodopsin is also charged.
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Affiliation(s)
- Megan N Sandberg
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, USA
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9
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Frähmcke JS, Wanko M, Phatak P, Mroginski MA, Elstner M. The protonation state of Glu181 in rhodopsin revisited: interpretation of experimental data on the basis of QM/MM calculations. J Phys Chem B 2010; 114:11338-52. [PMID: 20698519 DOI: 10.1021/jp104537w] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structure and spectroscopy of rhodopsin have been intensely studied in the past decade both experimentally and theoretically; however, important issues still remain unresolved. Of central interest is the protonation state of Glu181, where controversial and contradictory experimental evidence has appeared. While FTIR measurements indicate this residue to be unprotonated, preresonance Raman and UV-vis spectra have been interpreted in favor of a protonated Glu181. Previous computational approaches were not able to resolve this issue, providing contradicting data as well. Here, we perform hybrid QM/MM calculations using DFT methods for the electronic ground state, MRCI methods for the electronically excited states, and a polarization model for the MM part in order to investigate this issue systematically. We constructed various active-site models for protonated as well as unprotonated Glu181, which were evaluated by computing NMR, IR, Raman, and UV-vis spectroscopic data. The resulting differences in the UV-vis and Raman spectra between protonated and unprotonated models are very subtle, which has two major consequences. First, the common interpretation of prior Raman and UV-vis experiments in favor of a neutral Glu181 appears questionable, as it is based on the assumption that a charge at the Glu181 location would have a sizable impact. Second, also theoretical results should be interpreted with care. Spectroscopic differences between the structural models must be related to modeling uncertainties and intrinsic methodological errors. Despite a detailed comparison of various rhodopsins and mutants and consistently favorite results with charged Glu181 models, we find merely weak evidence from UV-vis and Raman calculations. On the contrary, difference FTIR and NMR chemical shift measurements on Rh mutants are indicative of the protonation state of Glu181. Supported by our results, they provide strong and independent evidence for a charged Glu181.
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Affiliation(s)
- Jan S Frähmcke
- Institute for Physical and Theoretical Chemistry, TU Braunschweig, Hans-Sommer-Str. 10, D-38106 Braunschweig, Germany
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Sekharan S, Altun A, Morokuma K. QM/MM study of dehydro and dihydro β-ionone retinal analogues in squid and bovine rhodopsins: implications for vision in salamander rhodopsin. J Am Chem Soc 2010; 132:15856-9. [PMID: 20964383 DOI: 10.1021/ja105050p] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Visual pigment rhodopsin provides a decisive crossing point for interaction between organisms and environment. Naturally occurring visual pigments contain only PSB11 and 3,4-dehydro-PSB11 as chromophores. Therefore, the ability of visual opsin to discriminate between the retinal geometries is investigated by means of QM/MM incorporation of PSB11, 6-s-cis and 6-s-trans forms of 3,4-dehydro-PSB11, and 3,4-dehydro-5,6-dihydro-PSB11 and 5,6-dihydro-PSB11 analogues into squid and bovine rhodopsin environments. The analogue-protein interaction reveals the binding site of squid rhodopsin to be malleable and ductile, while that of bovine rhodopsin is rigid and stiff. On the basis of these studies, a tentative model of the salamander rhodopsin binding site is also proposed.
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Affiliation(s)
- Sivakumar Sekharan
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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Gebhard R, Courtin JML, Shadid JB, van Haveren J, van Haeringen CJ, Lugtenburg J. Synthesis of retinals labelled with 13C in the cyclohexene ring. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19891080602] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Gebhard R, van der Hoef K, Lefeber AWM, Erkelens C, Lugtenburg J. Synthesis and spectroscopy of (14′-13C)- and (15′-13C)spheroidene. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19901090604] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Spijker-Assink MB, Winkel C, Baldwin GS, Lugtenburg J. 5-Demethylretinal and its 5-2H, 7-2H2 and 5,7-2H2 isotopomers. Synthesis, photochemistry and spectroscopy. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19881070304] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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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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Röhrig UF, Sebastiani D. NMR Chemical Shifts of the Rhodopsin Chromophore in the Dark State and in Bathorhodopsin: A Hybrid QM/MM Molecular Dynamics Study. J Phys Chem B 2008; 112:1267-74. [DOI: 10.1021/jp075662q] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ute F. Röhrig
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Molecular Modeling Group, Genopode Building CH-1015 Lausanne, Switzerland, and Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Daniel Sebastiani
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Molecular Modeling Group, Genopode Building CH-1015 Lausanne, Switzerland, and Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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Lemaître V, Yeagle P, Watts A. Molecular dynamics simulations of retinal in rhodopsin: from the dark-adapted state towards lumirhodopsin. Biochemistry 2005; 44:12667-80. [PMID: 16171381 DOI: 10.1021/bi0506019] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of photointermediates and conformational changes observed in the retinal chromophore of bilayer-embedded rhodopsin during the early steps of the protein activation have been studied by molecular dynamics (MD) simulation. In particular, the lysine-bound retinal has been examined, focusing on its conformation in the dark-adapted state (10 ns) and on the early steps after the isomerization of the 11-cis bond to trans (up to 10 ns). The parametrization for the chromophore is based on a recent quantum study [Sugihara, M., Buss, V., Entel, P., Elstner, M., and Frauenheim, T. (2002) Biochemistry 41, 15259-15266] and shows good conformational agreement with recent experimental results. The isomerization, induced by switching the function governing the dihedral angle for the C11=C12 bond, was repeated with several different starting conformations. From the repeated simulations, it is shown that the retinal model exhibits a conserved activation pattern. The conformational changes are sequential and propagate outward from the C11=C12 bond, starting with isomerization of the C11=C12 bond, then a rotation of methyl group C20, and followed by increased fluctuations at the beta-ionone ring. The dynamics of these changes suggest that they are linked with photointermediates observed by spectroscopy. The exact moment when these events occur after the isomerization is modulated by the starting conformation, suggesting that retinal isomerizes through multiple pathways that are slightly different. The amplitudes of the structural fluctuations observed for the protein in the dark-adapted state and after isomerization of the retinal are similar, suggesting a subtle mechanism for the transmission of information from the chromophore to the protein.
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Affiliation(s)
- Vincent Lemaître
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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Furutani Y, Terakita A, Shichida Y, Kandori H. FTIR Studies of the Photoactivation Processes in Squid Retinochrome. Biochemistry 2005; 44:7988-97. [PMID: 15924417 DOI: 10.1021/bi050219w] [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: 11/29/2022]
Abstract
Retinochrome is a photoisomerase of the invertebrate visual system, which converts all-trans-retinal to the 11-cis configuration and supplies it to visual rhodopsin. In this paper, we studied light-induced structural changes in squid retinochrome by means of low-temperature UV-visible and Fourier transform infrared (FTIR) spectroscopy. In PC liposomes, lumi-retinochrome was stable in the wide temperature range between 77 and 230 K. High thermal stability of the primary intermediate in retinochrome is in contrast to the case in rhodopsins. FTIR spectroscopy suggested that the chromophore of lumi-retinochrome is in a relaxed planar 11-cis form, being consistent with its high thermal stability. The chromophore binding pocket of retinochrome appears to accommodate both all-trans and 11-cis forms without a large distortion, and limited protein structural changes between all-trans and 11-cis chromophores may be suitable for the function of retinochrome as a photoisomerase. The analysis of N-D and O-D stretching vibrations in D(2)O revealed that the hydrogen bond of the Schiff base is weaker in retinochrome than in bovine rhodopsin and bacteriorhodopsin, while retinochrome has a water molecule under strongly hydrogen-bonded conditions (O-D stretch at 2334 cm(-)(1)). The hydrogen bond of the water is further strengthened in lumi-retinochrome. The formation of meta-retinochrome accompanies deprotonation of the Schiff base, together with the peptide backbone alterations of alpha-helices, and possible formation of beta-sheets. It was found that the Schiff base proton is not transferred to its counterion, Glu181, but directly released to the aqueous phase in PC liposomes (pH 7.5). This suggests that the Schiff base environment is exposed to solvent in meta-retinochrome, which may be advantageous for the hydrolysis reaction of the Schiff base in the transport of 11-cis-retinal to its shuttle protein.
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Affiliation(s)
- Yuji Furutani
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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Saam J, Tajkhorshid E, Hayashi S, Schulten K. Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin. Biophys J 2002; 83:3097-112. [PMID: 12496081 PMCID: PMC1302389 DOI: 10.1016/s0006-3495(02)75314-9] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Retinal cis-trans isomerization and early relaxation steps have been studied in a 10-ns molecular dynamics simulation of a fully hydrated model of membrane-embedded rhodopsin. The isomerization, induced by transiently switching the potential energy function governing the C(11)==C(12) dihedral angle of retinal, completes within 150 fs and yields a strongly distorted retinal. The most significant conformational changes in the binding pocket are straightening of retinal's polyene chain and separation of its beta-ionone ring from Trp-265. In the following 500 ps, transition of 6s-cis to 6s-trans retinal and dramatic changes in the hydrogen bonding network of the binding pocket involving the counterion for the protonated Schiff base, Glu-113, occur. Furthermore, the energy initially stored internally in the distorted retinal is transformed into nonbonding interactions of retinal with its environment. During the following 10 ns, increased mobilities of some parts of the protein, such as the kinked regions of the helices, mainly helix VI, and the intracellular loop I2, were observed, as well as transient structural changes involving the conserved salt bridge between Glu-134 and Arg-135. These features prepare the protein for major structural transformations achieved later in the photocycle. Retinal's motion, in particular, can be compared to an opening turnstile freeing the way for the proposed rotation of helix VI. This was demonstrated by a steered molecular dynamics simulation in which an applied torque enforced the rotation of helix VI.
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Affiliation(s)
- Jan Saam
- Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Avenue, Urbana, IL 61801, USA
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Röhrig UF, Guidoni L, Rothlisberger U. Early steps of the intramolecular signal transduction in rhodopsin explored by molecular dynamics simulations. Biochemistry 2002; 41:10799-809. [PMID: 12196019 DOI: 10.1021/bi026011h] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present molecular dynamics simulations of bovine rhodopsin in a membrane mimetic environment based on the recently refined X-ray structure of the pigment. The interactions between the protonated Schiff base and the protein moiety are explored both with the chromophore in the dark-adapted 11-cis and in the photoisomerized all-trans form. Comparison of simulations with Glu181 in different protonation states strongly suggests that this loop residue located close to the 11-cis bond bears a negative charge. Restrained molecular dynamics simulations also provide evidence that the protein tightly confines the absolute conformation of the retinal around the C12-C13 bond to a positive helicity. 11-cis to all-trans isomerization leads to an internally strained chromophore, which relaxes after a few nanoseconds by a switching of the ionone ring to an essentially planar all-trans conformation. This structural transition of the retinal induces in turn significant conformational changes of the protein backbone, especially in helix VI. Our results suggest a possible molecular mechanism for the early steps of intramolecular signal transduction in a prototypical G-protein-coupled receptor.
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Affiliation(s)
- Ute F Röhrig
- Laboratory of Inorganic Chemistry, Swiss Federal Institute of Technology, CH-8093 Zurich, Switzerland
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20
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Creemers AFL, Kiihne S, Bovee-Geurts PHM, DeGrip WJ, Lugtenburg J, de Groot HJM. (1)H and (13)C MAS NMR evidence for pronounced ligand-protein interactions involving the ionone ring of the retinylidene chromophore in rhodopsin. Proc Natl Acad Sci U S A 2002; 99:9101-6. [PMID: 12093898 PMCID: PMC123100 DOI: 10.1073/pnas.112677599] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2001] [Indexed: 11/18/2022] Open
Abstract
Rhodopsin is a member of the superfamily of G-protein-coupled receptors. This seven alpha-helix transmembrane protein is the visual pigment of the vertebrate rod photoreceptor cells that mediate dim light vision. In the active binding site of this protein the ligand or chromophore, 11-cis-retinal, is covalently bound via a protonated Schiff base to lysine residue 296. Here we present the complete (1)H and (13)C assignments of the 11-cis-retinylidene chromophore in its ligand-binding site determined with ultra high field magic angle spinning NMR. Native bovine opsin was regenerated with 99% enriched uniformly (13)C-labeled 11-cis-retinal. From the labeled pigment, (13)C carbon chemical shifts could be obtained by using two-dimensional radio frequency-driven dipolar recoupling in a solid-state magic angle spinning homonuclear correlation experiment. The (1)H chemical shifts were assigned by two-dimensional heteronuclear ((1)H-(13)C) dipolar correlation spectroscopy with phase-modulated Lee-Goldburg homonuclear (1)H decoupling applied during the t(1) period. The data indicate nonbonding interactions between the protons of the methyl groups of the retinylidene ionone ring and the protein. These nonbonding interactions are attributed to nearby aromatic acid residues Phe-208, Phe-212, and Trp-265 that are in close contact with, respectively, H-16/H-17 and H-18. Furthermore, binding of the chromophore involves a chiral selection of the ring conformation, resulting in equatorial and axial positions for CH(3)-16 and CH(3)-17.
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Affiliation(s)
- Alain F L Creemers
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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21
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Fujimoto Y, Fishkin N, Pescitelli G, Decatur J, Berova N, Nakanishi K. Solution and biologically relevant conformations of enantiomeric 11-cis-locked cyclopropyl retinals. J Am Chem Soc 2002; 124:7294-302. [PMID: 12071738 DOI: 10.1021/ja020083e] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To gain information on the conformation of the 11-cis-retinylidene chromophore bound to bovine opsin, the enantiomeric pair (2a and 2b) of 11-cis-locked bicyclo[5.1.0]octyl retinal (retCPr) 2 was prepared and its conformation was investigated by NMR, geometry optimization, and CD calculations. This compound is also of interest since it contains a unique moiety in which a chiral cyclopropyl group is flanked by triene and enal chromophores, and hence would clarify the little-known chiroptical contribution of a cyclopropyl ring linked to polyene systems. NMR revealed that the seven-membered ring of retCPr adopts a twist chair conformation. The NMR-derived structure constraints were then used for optimizing the geometry of 2 with molecular mechanics and ab initio methods. This revealed that enantiomer 2a with a 11 beta,12 beta-cyclopropyl group exists as two populations of diastereomers depending on the twist around the 6-s bond; however, the sense of twist around the 12-s is positive in both rotamers. The theoretical Boltzmann-weighted CD obtained with the pi-SCF-CI-DV MO method and experimental spectra were consistent, thus suggesting that the conjugative effect of the cyclopropyl moiety is minimal. It was found that only the beta-cyclopropyl enantiomer 2a, but not the alpha-enantiomer 2b, binds to opsin. This observation, together with earlier retinal analogues incorporation results, led to the conclusion that the chromophore sinks into the N-terminal of the opsin receptor from the side of the 4-methylene and 15-aldehyde, and that the binding cleft accommodates 11-cis-retinal with a slightly positive twist around C12/C13. A reinterpretation of the previously published negative CD couplet of 11,12-dihydrorhodopsin also leads to a chromophoric C12/C13 twist conformation with the 13-Me in front as in 1b. Such a conformation for the chromophore accounts for both the observed biostereoselectivity of retCPr 2a and the observed negative couplet of 11,12-dihydro-Rh7.
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Affiliation(s)
- Yukari Fujimoto
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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22
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Fujimoto Y, Ishihara J, Maki S, Fujioka N, Wang T, Furuta T, Fishkin N, Borhan B, Berova N, Nakanishi K. On the bioactive conformation of the rhodopsin chromophore: absolute sense of twist around the 6-s-cis bond. Chemistry 2001; 7:4198-204. [PMID: 11686599 DOI: 10.1002/1521-3765(20011001)7:19<4198::aid-chem4198>3.0.co;2-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Incubation of opsin with synthetic 6-s-locked retinoids 2a and 2b only led to pigment formation from the alpha-locked 2a, the CD spectrum of which was similar to that of native rhodopsin (Rh). This establishes that the 6-s-bond of the chromophore in rhodopsin is cis, and that its helicity is negative. Earlier cross-linking studies showed that the 11-cis to all-trans photoisomerization occurring in the batho-Rh to lumi-Rh conversion induces a flip over of the side carrying the ring moiety. The GTP-binding assay of pigment Rh-(2a), incorporating retinal analogue 2a, has shown that its activity is 80% that of the native pigment. That is, the overall conformation around the 6-s bond is retained in the steps leading to G-protein activation.
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Affiliation(s)
- Y Fujimoto
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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23
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DeGrip WJ, DeLange F, Klaassen CH, Verdegem PJ, Wallace-Williams S, Creemers AF, Bergo V, Bovee PH, Raap J, Rothschild KJ, DeGroot HJ, Lugtenburg J. Photoactivation of rhodopsin: interplay between protein and chromophore. ACTA ACUST UNITED AC 2000; 224:102-18; discussion 118-23. [PMID: 10614048 DOI: 10.1002/9780470515693.ch7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Data in the literature suggest a finely tuned interaction between ligand (11-cis-retinal) and protein (opsin) in order to allow very efficient photoactivation of the ligand and highly vectorial rhodopsin activation with a huge increase in receptor activity. We have further investigated this interaction using ligand homologues, 13C-ligand labelling or 15N-protein labelling, in combination with Fourier transform infrared (FT-IR) and solid-state magic angle spinning (ss-MAS)-NMR spectroscopy. Using 1D rotational resonance (RR) or double-quantum heteronuclear local field (2Q-HLF) ss-MAS-NMR we report the first structure refinement of the rhodopsin chromophore in situ. These measurements yield a specification of the torsional strain in the for isomerization essential C10-C13 segment of the chromophore. This strain is thought to contribute to the high rate and stereospecificity of the photoisomerization reaction. In agreement with previous data, the C10-C13 segment region reaches a relaxed all-trans configuration at the lumirhodopsin photointermediate. MAS-NMR analysis of [15N]lysine-labelled rhodopsin reveals the presence of a 'soft' counterion, requiring intermediate water molecules for stabilization. FT-IR studies on [2H]tyrosine-labelled rhodopsin demonstrate participation of several tyrosin(at)e residues in receptor activation. One of these, probably Tyr268, is already active at the bathorhodopsin stage. Finally, the effect of ligands with single additional methyl substituents in the C10-C12 region has been investigated. They do not affect the general activation pathway, but perturb the activation kinetics of rhodopsin, suggesting steric interference with protein residues. Possible implications of these results for a structural role of water residues will be discussed, as well.
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Affiliation(s)
- W J DeGrip
- University of Nijmegen, Department of Biochemistry, The Netherlands
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24
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Mathies R, Lugtenburg J. Chapter 2 The primary photoreaction of rhodopsin. HANDBOOK OF BIOLOGICAL PHYSICS 2000. [DOI: 10.1016/s1383-8121(00)80005-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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25
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Degrip W, Rothschild K. Chapter 1 Structure and mechanism of vertebrate visual pigments. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1383-8121(00)80004-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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26
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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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27
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Hsieh CH, Sue SC, Lyu PC, Wu WG. Membrane packing geometry of diphytanoylphosphatidylcholine is highly sensitive to hydration: phospholipid polymorphism induced by molecular rearrangement in the headgroup region. Biophys J 1997; 73:870-7. [PMID: 9251804 PMCID: PMC1180984 DOI: 10.1016/s0006-3495(97)78120-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Diphytanoylphosphatidylcholine (DPhPC) has often been used in the study of protein-lipid interaction and membrane channel activity, because of the general belief that it has high bilayer stability, low ion leakage, and fatty acyl packing comparable to that of phospholipid bilayers in the liquid-crystalline state. In this solid-state 31P and 2H NMR study, we find that the membrane packing geometry and headgroup orientation of DPhPC are highly sensitive to the temperature studied and its water content. The phosphocholine headgroup of DPhPC starts to change its orientation at a water content as high as approximately 16 water molecules per lipid, as evidenced by hydration-dependent 2H NMR study at room temperature. In addition, a temperature-induced structural transition in the headgroup orientation is detected in the temperature range of approximately 20-60 degrees C for lipids with approximately 8-11 water molecules per DPhPC. Dehydration of the lipid by one more water molecule leads to a nonlamellar, presumably cubic, phase formation. The lipid packing becomes a hexagonal phase at approximately 6 water molecules per lipid. A phase diagram of DPhPC in the temperature range of -40 degrees C to 80 degrees C is thus constructed on the basis of NMR results. The newly observed hydration-dependent DPhPC lipid polymorphism emphasizes the importance of molecular packing in the headgroup region in modulating membrane structure and protein-induced pore formation of the DPhPC bilayer.
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Affiliation(s)
- C H Hsieh
- Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
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28
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Pogozheva ID, Lomize AL, Mosberg HI. The transmembrane 7-alpha-bundle of rhodopsin: distance geometry calculations with hydrogen bonding constraints. Biophys J 1997; 72:1963-85. [PMID: 9129801 PMCID: PMC1184393 DOI: 10.1016/s0006-3495(97)78842-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A 3D model of the transmembrane 7-alpha-bundle of rhodopsin-like G-protein-coupled receptors (GPCRs) was calculated using an iterative distance geometry refinement with an evolving system of hydrogen bonds, formed by intramembrane polar side chains in various proteins of the family and collectively applied as distance constraints. The alpha-bundle structure thus obtained provides H bonding of nearly all buried polar side chains simultaneously in the 410 GPCRs considered. Forty evolutionarily conserved GPCR residues form a single continuous domain, with an aliphatic "core" surrounded by six clusters of polar and aromatic side chains. The 7-alpha-bundle of a specific GPCR can be calculated using its own set of H bonds as distance constraints and the common "average" model to restrain positions of the helices. The bovine rhodopsin model thus determined is closely packed, but has a few small polar cavities, presumably filled by water, and has a binding pocket that is complementary to 11-cis (6-s-cis, 12-s-trans, C = N anti)-retinal or to all-trans-retinal, depending on conformations of the Lys296 and Trp265 side chains. A suggested mechanism of rhodopsin photoactivation, triggered by the cis-trans isomerization of retinal, involves rotations of Glu134, Tyr223, Trp265, Lys296, and Tyr306 side chains and rearrangement of their H bonds. The model is in agreement with published electron cryomicroscopy, mutagenesis, chemical modification, cross-linking, Fourier transform infrared spectroscopy, Raman spectroscopy, electron paramagnetic resonance spectroscopy, NMR, and optical spectroscopy data. The rhodopsin model and the published structure of bacteriorhodopsin have very similar retinal-binding pockets.
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Affiliation(s)
- I D Pogozheva
- College of Pharmacy, University of Michigan, Ann Arbor 48109, USA
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29
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Abstract
For the first time the total synthesis of the peptaibol zervamicin IIB is described. Synthesis of this peptaibol was achieved by the Fmoc/tert-butyl strategy in solution using a fragment condensation approach. Three fragments of zervamicin IIB were obtained by stepwise elongation with Fmoc amino acids using BOP as a coupling reagent. For the introduction of the highly sterically hindered alpha-aminoisobutyric acid residues BOP/DMAP activation was applied. The fmoc group was removed by reaction with 0.1 M NaOH in dioxane/methanol/water (30/9/1, v/v/v). Peptide fragments were coupled by means of a new coupling reagent, CF3-PyBOP. Using the strategy developed, zervamicin IIB and two analogues specifically deuterium-labelled at different positions of the glutamine-11 residue have been synthesized in 40% overall yield based on the isotopically labelled amino acid and with 98 +/- 2% of isotope enrichment. FAB mass spectroscopy, 600 MHz 1H-NMR spectroscopy and high-performance liquid chromatography provided convincing evidence that the synthetic products, zervamicin IIB and its deuterium-labelled analogues, fully correspond to the naturally occurring zervamicin IIB.
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Affiliation(s)
- A Ogrel
- Leiden Institute of Chemistry, Leiden University, The Netherlands
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30
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Ogrel A, Bloemhoff W, Lugtenburg J, Raap J. Synthesis of the Isotopically LabelledC-Terminal Fragment of Zervamicin: An Approach to the Synthesis of Aib-Containing Peptides. ACTA ACUST UNITED AC 1997. [DOI: 10.1002/jlac.199719970109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Houjou H, Sakurai M, Asakawa N, Inoue Y, Tamura Y. Ab InitioStudy of13C Shieldings for Linear π-Conjugated Systems. Theoretical Determination of the C12−C13 Conformation in the Chromophore of Rhodopsin. J Am Chem Soc 1996. [DOI: 10.1021/ja961023+] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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Houjou H, Sakurai M, Asakawa N, Inoue Y, Tamura Y, Watanabe Y. Ab initioStudy of the C12-C13 Conformation of 11- cis-retinal. CHEM LETT 1995. [DOI: 10.1246/cl.1995.1039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Watts A, Ulrich AS, Middleton DA. Membrane protein structure: the contribution and potential of novel solid state NMR approaches. Mol Membr Biol 1995; 12:233-46. [PMID: 8520624 DOI: 10.3109/09687689509072423] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Alternative methods for describing molecular detail for large integral membrane proteins are required in the absence of routine crystallographic approaches. Novel solid state NMR methods, devised for the study of large molecular assemblies, are now finding applications in biological systems, including integral membrane proteins. Wild-type and genetically engineered proteins can be investigated and detailed information about side chains, prosthetic groups, ligands (e.g. drugs) and binding sites can be deduced. The molecular structure and dynamics of selected parts of the proteins are accessible by a range of different solid state NMR approaches. Inter- and intra-atomic distances can be determined rather accurately (within ångströms) and the orientation of molecular bonds (within 2 degrees) can be measured in ideal cases. Here, a brief description of the methods is given and then some specific examples described with an indication of the future potential for the approaches in studying membrane proteins. It is anticipated that this emerging NMR methodology will be more widely used in the future, not only for resolving local structure, but also for more expansive descriptions of membrane protein structure at atomic resolution.
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Affiliation(s)
- A Watts
- Department of Biochemistry, University of Oxford, UK
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34
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Fasman GD. The measurement of transmembrane helices by the deconvolution of CD spectra of membrane proteins: A review. Biopolymers 1995. [DOI: 10.1002/bip.360370505] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Beppu Y, Kakitani T. THEORETICAL STUDY OF COLOR CONTROL MECHANISM IN RETINAL PROTEINS.: I. ROLE OF THE TRYPTOPHAN RESIDUE, TYROSINE RESIDUE AND WATER MOLECULE. Photochem Photobiol 1994. [DOI: 10.1111/j.1751-1097.1994.tb09673.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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36
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Beppu Y, Kakitani T. THEORETICAL STUDY OF COLOR CONTROL MECHANISM IN RETINAL PROTEINS. I. ROLE OF THE TRYPTOPHAN RESIDUE, TYROSINE RESIDUE and WATER MOLECULE. Photochem Photobiol 1994. [DOI: 10.1111/j.1751-1097.1994.tb08235.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Kinumi T, Tsujimoto K, Ohashi M, Hara R, Hara T, Ozaki K, Sakai M, Katsuta Y, Wada A, Ito M. The conformational analysis and photoisomerization of retinochrome analogs with polyenals. Photochem Photobiol 1993; 58:409-12. [PMID: 8234476 DOI: 10.1111/j.1751-1097.1993.tb09582.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
3,7-Dimethyl-2,4,6,8,10-dodecapentaenal was synthesized for reconstitution of the retinochrome analog. Its opsin shift was 1000 cm-1 smaller than that of native retinochrome, whose chromophore contains the same number of double bonds. The conformational change from 6-s-trans to 6-s-cis, as figured in a retinal molecule, plays an important role in the formation of the retinochrome analog, based on the estimation of opsin shifts for retinal analogs locked in the 6-s conformation. Thus the conformation of the 6-7 single bond in the native retinochrome was suggested to be 6-s-cis. Analysis of the circular dichroic spectra of retinochrome analogs revealed that the 6-s conformation is independent of the appearance of the beta-band. The stereoselectivity in the photoisomerization of the retinal analogs by a retinochrome template depends on the hydrophobic binding in the region of the beta-ionone ring.
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Affiliation(s)
- T Kinumi
- Department of Applied Physics and Chemistry, University of Electro-Communications, Tokyo, Japan
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38
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Han M, DeDecker BS, Smith SO. Localization of the retinal protonated Schiff base counterion in rhodopsin. Biophys J 1993; 65:899-906. [PMID: 8105993 PMCID: PMC1225790 DOI: 10.1016/s0006-3495(93)81117-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Semiempirical molecular orbital calculations are combined with 13C NMR chemical shifts to localize the counterion in the retinal binding site of vertebrate rhodopsin. Charge densities along the polyene chain are calculated for an 11-cis-retinylidene protonated Schiff base (11-cis-RPSB) chromophore with 1) a chloride counterion at various distances from the Schiff base nitrogen, 2) one or two chloride counterions at different positions along the retinal chain from C10 to C15 and at the Schiff base nitrogen, and 3) a carboxylate counterion out of the retinal plane near C12. Increasing the distance of the negative counterion from the Schiff base results in an enhancement of alternating negative and positive partial charge on the even- and odd-numbered carbons, respectively, when compared to the 11-cis-RPSB chloride model compound. In contrast, the observed 13C NMR data of rhodopsin exhibit downfield chemical shifts from C8 to C13 relative to the 11-cis-RPSB.Cl corresponding to a net increase of partial positive or decrease of partial negative charge at these positions (Smith, S. O., I. Palings, M. E. Miley, J. Courtin, H. de Groot, J. Lugtenburg, R. A. Mathies, and R. G. Griffin. 1990. Biochemistry. 29:8158-8164). The anomalous changes in charge density reflected in the rhodopsin NMR chemical shifts can be qualitatively modeled by placing a single negative charge above C12. The calculated fit improves when a carboxylate counterion is used to model the retinal binding site. Inclusion of water in the model does not alter the fit to the NMR data, although it is consistent with observations based on other methods. These data constrain the location and the orientation of the Glu113 side chain, which is known to be the counterion in rhodopsin, and argue for a strong interaction centered at C12 of the retinylidene chain.
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Affiliation(s)
- M Han
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
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39
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Park K, Perczel A, Fasman GD. Differentiation between transmembrane helices and peripheral helices by the deconvolution of circular dichroism spectra of membrane proteins. Protein Sci 1992; 1:1032-49. [PMID: 1338977 PMCID: PMC2142169 DOI: 10.1002/pro.5560010809] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The interpretation of the circular dichroism (CD) spectra of proteins to date requires additional secondary structural information of the proteins to be analyzed, such as X-ray or NMR data. Therefore, these methods are inappropriate for a CD database whose secondary structures are unknown, as in the case of the membrane proteins. The convex constraint analysis algorithm (Perczel, A., Hollósi, M., Tusnády, G., & Fasman, G. D., 1991, Protein Eng. 4, 669-679), on the other hand, operates only on a collection of spectral data to extract the common spectral components with their spectral weights. The linear combinations of these derived "pure" CD curves can reconstruct the original data set with great accuracy. For a membrane protein data set, the five-component spectra so obtained from the deconvolution consisted of two different types of alpha helices (the alpha helix in the soluble domain and the alpha T helix, for the transmembrane alpha helix), a beta-pleated sheet, a class C-like spectrum related to beta turns, and a spectrum correlated with the unordered conformation. The deconvoluted CD spectrum for the alpha T helix was characterized by a positive red-shifted band in the range 195-200 nm (+95,000 deg cm2 dmol-1), with the intensity of the negative band at 208 nm being slightly less negative than that of the 222-nm band (-50,000 and -60,000 deg cm2 dmol-1, respectively) in comparison with the regular alpha helix, with a positive band at 190 nm and two negative bands at 208 and 222 nm with magnitudes of +70,000, -30,000, and -30,000 deg cm2 dmol-1, respectively.
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Affiliation(s)
- K Park
- Graduate Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02154
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40
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Abstract
From a 19F-NMR study of 9,11-dicis-12-fluororhodopsin and its photobleached product, we concluded that the initially formed chromophore retained its configuration and the photoproduct corresponded to the two-bond isomerized all-trans. Upon standing, it slowly isomerized to the 9-cis isomer. The method represents a direct, non-destructive procedure for determining configuration purity of the pigment formed. Its unique fluorine opsin shift value is consistent with the expected different orientation of the fluoro-substituent in a dicis pigment.
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Affiliation(s)
- L U Colmenares
- Department of Chemistry, University of Hawaii, Honolulu 96822
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41
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Abstract
A review is given of the use of nuclear magnetic resonance (NMR) spectroscopy to study bacteriorhodopsin and bovine rhodopsin. Solution and solid-state approaches are included. The studies of the bacterial proton pump examine the chromophore, the peptide backbone, and the protein side chains. The studies of the bovine visual pigment are limited to the chromophore. Various forms of each pigment are considered. Both structural and dynamic features are addressed.
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Affiliation(s)
- L Zheng
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02254-9110
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42
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Lawson MA, Zacks DN, Derguini F, Nakanishi K, Spudich JL. Retinal analog restoration of photophobic responses in a blind Chlamydomonas reinhardtii mutant. Evidence for an archaebacterial like chromophore in a eukaryotic rhodopsin. Biophys J 1991; 60:1490-8. [PMID: 1777569 PMCID: PMC1260207 DOI: 10.1016/s0006-3495(91)82184-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The strain CC-2359 of the unicellular eukaryotic alga Chlamydomonas reinhardtii originally described as a low pigmentation mutant is found to be devoid of photophobic stop responses to photostimuli over a wide range of light intensities. Photophobic responses of the mutant are restored by exogenous addition of all-trans retinal. We have combined computer-based cell-tracking and motion analysis with retinal isomer and retinal analog reconstitution of CC-2359 to investigate properties of the photophobic response receptor. Most rapid and most complete reconstitution is obtained with all-trans retinal compared to 13-cis, 11-cis, and 9-cis retinal. An analog locked by a carbon bridge in a 6-s-trans conformation reconstitutes whereas the corresponding 6-s-cis locked analog does not. Retinal analogs prevented from isomerization around the 13-14 double bond by a five-membered ring in the polyene chain (locked in either the 13-trans or 13-cis configuration) do not restore the response, but enter the chromophore binding pocket as evidenced by their inhibition of all-trans retinal regeneration of the response. Results of competition experiments between all-trans and each of the 13-locked analogs fit a model in which each chromophore exhibits reversible binding to the photoreceptor apoprotein. A competitive inhibition scheme closely fits the data and permits calculation of apparent dissociation constants for the in vivo reconstitution process of 2.5 x 10(-11) M, 5.2 x 10(-10) M, and 5.4 x 10(-9) M, for all-trans, 13-trans-locked and 13-cis-locked analogs, respectively. The chromophore requirement for the trans configuration and 6-s-trans conformation, and the lack of signaling function from analogs locked at the 13 position, are characteristic of archaebacterial rhodopsins, rather than the previously studied eukaryotic rhodopsins (i.e., visual pigments).
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Affiliation(s)
- M A Lawson
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461
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43
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Affiliation(s)
- P F Knowles
- Department of Biochemistry and Molecular Biology, University of Leeds, U.K
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44
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Smith SO, Palings I, Miley ME, Courtin J, de Groot H, Lugtenburg J, Mathies RA, Griffin RG. Solid-state NMR studies of the mechanism of the opsin shift in the visual pigment rhodopsin. Biochemistry 1990; 29:8158-64. [PMID: 2261469 DOI: 10.1021/bi00487a025] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Solid-state 13C NMR spectra have been obtained of bovine rhodopsin and isorhodopsin regenerated with retinal selectively 13C labeled along the polyene chain. In rhodopsin, the chemical shifts for 13C-5, 13C-6, 13C-7, 13C-14, and 13C-15 correspond closely to the chemical shifts observed in the 11-cis protonated Schiff base (PSB) model compound. Differences in chemical shift relative to the 11-cis PSB chloride salt are observed for positions 8 through 13, with the largest deshielding (6.2 ppm) localized at position 13. The localized deshielding at C-13 supports previous models of the opsin shift in rhodopsin that place a protein perturbation in the vicinity of position 13. Spectra obtained of isorhodopsin regenerated with 13C-labeled 9-cis-retinals reveal large perturbations at 13C-7 and 13C-13. The similar deshielding of the 13C-13 resonance in both pigments supports the presence of a protein perturbation near position 13. However, the chemical shifts at positions 7 and 12 in isorhodopsin are not analogous to those observed in rhodopsin and suggest that the binding site interactions near these positions are different for the two pigments. The implications of these results for the mechanism of the opsin shift in these proteins are discussed.
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Affiliation(s)
- S O Smith
- Francis Bitter National Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139
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45
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Makino CL, Kraft TW, Mathies RA, Lugtenburg J, Miley ME, van der Steen R, Baylor DA. Effects of modified chromophores on the spectral sensitivity of salamander, squirrel and macaque cones. J Physiol 1990; 424:545-60. [PMID: 2391661 PMCID: PMC1189828 DOI: 10.1113/jphysiol.1990.sp018082] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
1. Chemically modified retinal chromophores were used to investigate the mechanisms that produce the characteristic spectral absorptions of cone pigments. Spectral sensitivities of single cones from the salamander, squirrel and macaque retina were determined by electrical recording. The chromophore was then replaced by bleaching the pigment and regenerating it with a retinal analogue. 2. Exposing a bleached cone to 9-cis-retinal for a brief period (less than 20 min) caused its flash sensitivity to recover to about 0.2 of the pre-bleach value. Similar exposure to a locked 6-s-cis, 9-cis analogue gave a recovery to about 0.03 of the pre-bleach value. 3. Unlike the flash sensitivity, the saturating photocurrent amplitude often recovered completely after bleaching and regenerating the pigment. 4. When the 3-dehydroretinal chromophore in the salamander long-wavelength-sensitive (red) cone was replaced with 11-cis-retinal, shortening the conjugated chain in the chromophore, the spectral sensitivity underwent a blue shift of 67 nm. 5. Pigments containing the planar-locked 6-s-cis.9-cis-retinal analogue absorbed at substantially longer wavelength than those containing unmodified 9-cis-retinal. The opsin shift, a measure of the protein's ability to modify the chromophore's absorption was larger for the locked analogue than for 9-cis-retinal. This suggests that the native chromophore assumes a twisted 6-s-cis conformation in these pigments. 6. The spectral sensitivities of red and green macaque cones containing 9-cis-retinal or planar-locked 6-s-cis.9-cis-retinal retained the 30 nm separation characteristic of the native pigments. This suggests that the different absorptions of of the 6-7 carbon bond in the retinal chromophore.
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Affiliation(s)
- C L Makino
- Department of Neurobiology, Stanford Medical School, CA 94305
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46
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Fukada Y, Okano T, Shichida Y, Yoshizawa T, Trehan A, Mead D, Denny M, Asato AE, Liu RS. Comparative study on the chromophore binding sites of rod and red-sensitive cone visual pigments by use of synthetic retinal isomers and analogues. Biochemistry 1990; 29:3133-40. [PMID: 2140051 DOI: 10.1021/bi00464a033] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A comparative study on the chromophore (retinal) binding sites of the opsin (R-photopsin) from chicken red-sensitive cone visual pigment (iodopsin) and that scotopsin) from bovine rod pigment (rhodopsin) was made by the aid of geometric isomers of retinal (all-trans, 13-cis, 11-cis, 9-cis, and 7-cis) and retinal analogues including fluorinated (14-F, 12-F, 10-F, and 8-F) and methylated (12-methyl) 11-cis-retinals. The stereoselectivity of R-photopsin for the retinal isomers and analogues was almost identical with that of scotopsin, indicating that the shapes of the chromophore binding sites of both opsins are similar, although the former appears to be somewhat more restricted than the latter. The rates of pigment formation from R-photopsin were considerably greater than those from scotopsin. In addition, all the iodopsin isomers and analogues were more susceptible to hydroxylamine than were the rhodopsin ones. These observations suggest that the retinal binding site of iodopsin is located near the protein surface. On the basis of the spectral properties of fluorinated analogues, a polar group in the chromophore binding site of iodopsin as well as rhodopsin was estimated to be located near the hydrogen atom at the C10 position of the retinylidene chromophore. A large difference in wavelength between the absorption maxima of iodopsin and rhodopsin was significantly reduced in the 9-cis and 7-cis pigments. On the assumption that the retinylidene chromophore is anchored rigidly at the alpha-carbon of the lysine residue and loosely at the cyclohexenyl ring, each of the two isomers would have the Schiff-base nitrogen at a position altered from that of the 11-cis pigments.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- Y Fukada
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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47
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Ottolenghi M, Sheves M. Synthetic retinals as probes for the binding site and photoreactions in rhodopsins. J Membr Biol 1989; 112:193-212. [PMID: 2693733 DOI: 10.1007/bf01870951] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- M Ottolenghi
- Department of Physical Chemistry, Hebrew University of Jerusalem, Israel
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48
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Sakmar TP, Franke RR, Khorana HG. Glutamic acid-113 serves as the retinylidene Schiff base counterion in bovine rhodopsin. Proc Natl Acad Sci U S A 1989; 86:8309-13. [PMID: 2573063 PMCID: PMC298270 DOI: 10.1073/pnas.86.21.8309] [Citation(s) in RCA: 506] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The characteristic wavelength at which a visual pigment absorbs light is regulated by interactions between protein (opsin) and retinylidene Schiff base chromophore. By using site-directed mutagenesis, charged amino acids in bovine rhodopsin transmembrane helix C were systematically replaced. Substitution of glutamic acid-134 or arginine-135 did not affect spectral properties. However, substitution of glutamic acid-122 by glutamine or by aspartic acid formed pigments that were blue-shifted in light absorption (lambda max = 480 nm and 475 nm, respectively). While the substitution of glutamic acid-113 by aspartic acid gave a slightly red-shifted pigment (lambda max = 505 nm), replacement by glutamine formed a pigment that was strikingly blue-shifted in light absorption (lambda max = 380 nm). The 380-nm species existed in a pH-dependent equilibrium with a 490-nm species such that at acidic pH all of the pigment was converted to lambda max = 490 nm. We conclude that glutamic acid-113 serves as the retinylidene Schiff base counterion in rhodopsin. We believe that this opsin-chromophore interaction is an example of a general mechanism of color regulation in the visual pigments.
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Affiliation(s)
- T P Sakmar
- Department of Biology, Massachusetts Institute of Technology, Cambridge 01239
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49
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Chen JG, Nakamura T, Ebrey TG, Ok H, Konno K, Derguini F, Nakanishi K, Honig B. Wavelength regulation in iodopsin, a cone pigment. Biophys J 1989; 55:725-9. [PMID: 2524224 PMCID: PMC1330556 DOI: 10.1016/s0006-3495(89)82871-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The opsin shift, the difference in wavenumber between the absorption peak of a visual pigment and the protonated Schiff base of the chromophore, represents the influence of the opsin binding site on the chromophore. The opsin shift for the chicken cone pigment iodopsin is much larger than that for rhodopsin. To understand the origin of this opsin shift and the mechanism of wavelength regulation in iodopsin, a series of synthetic 9-cis and 11-cis dehydro- and dihydro-retinals was used to regenerate iodopsin-based pigments. The opsin shifts of these pigments are quite similar to those found in bacteriorhodopsin-based artificial pigments. On the basis of these studies, a tentative model of wavelength regulation in iodopsin is proposed.
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Affiliation(s)
- J G Chen
- University of Illinois, Department of Physiology and Biophysics, Urbana 61801
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50
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Koutalos Y, Ebrey TG, Tsuda M, Odashima K, Lien T, Park MH, Shimizu N, Derguini F, Nakanishi K, Gilson HR. Regeneration of bovine and octopus opsins in situ with natural and artificial retinals. Biochemistry 1989; 28:2732-9. [PMID: 2525050 DOI: 10.1021/bi00432a055] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We consider the problem of color regulation in visual pigments for both bovine rhodopsin (lambda max = 500 nm) and octopus rhodopsin (lambda max = 475 nm). Both pigments have 11-cis-retinal (lambda max = 379 nm, in ethanol) as their chromophore. These rhodopsins were bleached in their native membranes, and the opsins were regenerated with natural and artificial chromophores. Both bovine and octopus opsins were regenerated with the 9-cis- and 11-cis-retinal isomers, but the octopus opsin was additionally regenerated with the 13-cis and all-trans isomers. Titration of the octopus opsin with 11-cis-retinal gave an extinction coefficient for octopus rhodopsin of 27,000 +/- 3000 M-1 cm-1 at 475 nm. The absorption maxima of bovine artificial pigments formed by regenerating opsin with the 11-cis dihydro series of chromophores support a color regulation model for bovine rhodopsin in which the chromophore-binding site of the protein has two negative charges: one directly hydrogen bonded to the Schiff base nitrogen and another near carbon-13. Formation of octopus artificial pigments with both all-trans and 11-cis dihydro chromophores leads to a similar model for octopus rhodopsin and metarhodopsin: there are two negative charges in the chromophore-binding site, one directly hydrogen bonded to the Schiff base nitrogen and a second near carbon-13. The interaction of this second charge with the chromophore in octopus rhodopsin is weaker than in bovine, while in metarhodopsin it is as strong as in bovine.
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Affiliation(s)
- Y Koutalos
- Department of Physiology and Biophysics, University of Illinois, Urbana 61801
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